Moodle in English: Caprover upgrade fail

I used these Bitnami instructions to upgrade Moodle for my Caprover (Docker) system from V5.3.1 to 5.3.3.

This method has worked previously numerous times yet has now failed.

I get a loop when after it prints: Running database upgrade

2025-03-20T22:26:10.960122801Z moodle 22:26:10.95 INFO ==>
2025-03-20T22:26:10.966781094Z moodle 22:26:10.96 INFO ==> Welcome to the Bitnami moodle container
2025-03-20T22:26:10.967816489Z moodle 22:26:10.96 INFO ==> Subscribe to project updates by watching https://github.com/bitnami/containers
2025-03-20T22:26:10.970035633Z moodle 22:26:10.96 INFO ==> Submit issues and feature requests at https://github.com/bitnami/containers/issues
2025-03-20T22:26:10.972668187Z moodle 22:26:10.97 INFO ==> Upgrade to Tanzu Application Catalog for production environments to access custom-configured and pre-packaged software components. Gain enhanced features, including Software Bill of Materials (SBOM), CVE scan result reports, and VEX documents. To learn more, visit https://bitnami.com/enterprise
2025-03-20T22:26:10.974745012Z moodle 22:26:10.97 INFO ==>
2025-03-20T22:26:10.976501193Z moodle 22:26:10.97 INFO ==> ** Starting Moodle setup **
2025-03-20T22:26:11.034881626Z moodle 22:26:11.03 INFO ==> Generating sample certificates
2025-03-20T22:26:12.251341980Z Certificate request self-signature ok
2025-03-20T22:26:12.251404657Z subject=CN = example.com
2025-03-20T22:26:12.289101535Z realpath: /bitnami/apache/conf: No such file or directory
2025-03-20T22:26:12.295185796Z moodle 22:26:12.29 INFO ==> Configuring Apache ServerTokens directive
2025-03-20T22:26:12.339340524Z moodle 22:26:12.33 INFO ==> Configuring PHP options
2025-03-20T22:26:12.353281581Z moodle 22:26:12.35 INFO ==> Setting PHP expose_php option
2025-03-20T22:26:12.369399719Z moodle 22:26:12.36 INFO ==> Setting PHP max_execution_time option
2025-03-20T22:26:12.383632076Z moodle 22:26:12.38 INFO ==> Setting PHP max_input_time option
2025-03-20T22:26:12.399288590Z moodle 22:26:12.39 INFO ==> Setting PHP max_input_vars option
2025-03-20T22:26:12.414325998Z moodle 22:26:12.41 INFO ==> Setting PHP memory_limit option
2025-03-20T22:26:12.426537146Z moodle 22:26:12.42 INFO ==> Setting PHP post_max_size option
2025-03-20T22:26:12.441931728Z moodle 22:26:12.44 INFO ==> Setting PHP upload_max_filesize option
2025-03-20T22:26:12.453815129Z moodle 22:26:12.45 INFO ==> Setting PHP output_buffering option
2025-03-20T22:26:12.486524258Z moodle 22:26:12.48 INFO ==> Validating settings in MYSQL_CLIENT_* env vars
2025-03-20T22:26:12.496130787Z moodle 22:26:12.49 INFO ==> Validating settings in POSTGRESQL_CLIENT_* env vars
2025-03-20T22:26:12.632631421Z moodle 22:26:12.63 INFO ==> Restoring persisted Moodle installation
2025-03-20T22:26:15.393394552Z moodle 22:26:15.39 INFO ==> Trying to connect to the database server
2025-03-20T22:26:15.472767014Z moodle 22:26:15.47 INFO ==> Running database upgrade

Moodle directory permissions

Are the following permissions correct or incorrect for my Moodle directory?: ls -la total 1276 drwxrwxr-x 65 daemon daemon 4096 Feb 10 03:32 . drwxr-xr-x 6 barkingb barkingb 4096 Mar 20 22:43 .. drwxrwxr-x 16 daemon daemon 4096 Feb 7 13:18 admin drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 ai drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 analytics drwxrwxr-x 16 daemon daemon 4096 Feb 7 13:18 auth drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 availability drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 backup drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 badges -rw-rw-r-- 1 daemon daemon 311 Feb 7 13:18 behat.yml.dist drwxrwxr-x 48 daemon daemon 4096 Feb 7 13:18 blocks drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 blog -rw-rw-r-- 1 daemon daemon 1162 Feb 7 13:18 brokenfile.php drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 cache drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 calendar drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 cohort drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 comment drwxrwxr-x 6 daemon daemon 4096 Feb 7 13:18 communication drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 competency drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 completion -rw-rw-r-- 1 daemon daemon 2094 Feb 7 13:18 composer.json -rw-rw-r-- 1 daemon daemon 168233 Feb 7 13:18 composer.lock -rw-rw-r-- 1 daemon daemon 68644 Feb 7 13:18 config-dist.php -rw-r----- 1 root daemon 986 Dec 22 2023 config.php drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 contentbank -rw-rw-r-- 1 daemon daemon 2651 Feb 7 13:18 CONTRIBUTING.md -rw-rw-r-- 1 daemon daemon 35147 Feb 7 13:18 COPYING.txt drwxrwxr-x 10 daemon daemon 4096 Feb 7 13:18 course drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 customfield drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 dataformat -rw-rw-r-- 1 daemon daemon 2675 Feb 7 13:18 draftfile.php -rw-rw-r-- 1 daemon daemon 1382 Feb 7 13:18 editmode.php drwxrwxr-x 19 daemon daemon 4096 Feb 7 13:18 enrol drwxrwxr-x 2 daemon daemon 4096 Feb 7 13:18 error -rw-rw-r-- 1 daemon daemon 8426 Feb 7 13:18 .eslintrc drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 favourites -rw-rw-r-- 1 daemon daemon 3919 Feb 7 13:18 file.php drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 files drwxrwxr-x 18 daemon daemon 4096 Feb 7 13:18 filter -rw-rw-r-- 1 daemon daemon 597 Feb 7 13:18 .gherkin-lintrc -rw-rw-r-- 1 daemon daemon 142 Feb 7 13:18 .gitattributes -rw-rw-r-- 1 daemon daemon 953 Feb 7 14:42 githash.php drwxrwxr-x 3 daemon daemon 4096 Feb 7 13:18 .github drwxrwxr-x 11 daemon daemon 4096 Feb 7 13:18 grade drwxrwxr-x 6 daemon daemon 4096 Feb 7 13:18 group drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 .grunt -rw-rw-r-- 1 daemon daemon 9671 Feb 7 13:18 Gruntfile.js drwxrwxr-x 9 daemon daemon 4096 Feb 7 13:18 h5p -rw-rw-r-- 1 daemon daemon 1423 Feb 7 13:18 help_ajax.php -rw-rw-r-- 1 daemon daemon 1872 Feb 7 13:18 help.php -rw-rw-r-- 1 daemon daemon 5435 Feb 7 13:18 index.php drwxrwxr-x 3 daemon daemon 4096 Feb 7 13:18 install -rw-rw-r-- 1 daemon daemon 25849 Feb 7 13:18 install.php -rw-rw-r-- 1 daemon daemon 664 Feb 7 13:18 INSTALL.txt drwxrwxr-x 3 daemon daemon 4096 Feb 7 13:18 iplookup -rw-rw-r-- 1 daemon daemon 16 Feb 7 13:18 .jshintignore -rw-rw-r-- 1 daemon daemon 1545 Feb 7 13:18 .jshintrc drwxrwxr-x 3 daemon daemon 4096 Feb 7 13:18 lang drwxrwxr-x 75 daemon daemon 4096 Feb 7 13:18 lib drwxrwxr-x 2 daemon daemon 4096 Feb 7 13:18 local drwxrwxr-x 3 daemon daemon 4096 Feb 7 13:18 login drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 media drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 message drwxrwxr-x 6 daemon daemon 4096 Feb 7 13:18 mnet drwxrwxr-x 28 daemon daemon 4096 Feb 10 03:43 mod drwxrwxr-x 2 daemon daemon 4096 Feb 7 13:18 moodlenet drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 my drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 notes -rw-rw-r-- 1 daemon daemon 484761 Feb 7 13:18 npm-shrinkwrap.json -rw-rw-r-- 1 daemon daemon 8 Feb 7 13:18 .nvmrc -rw-rw-r-- 1 daemon daemon 1825 Feb 7 13:18 package.json drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 payment -rw-rw-r-- 1 daemon daemon 145 Feb 7 13:18 phpcs.xml.dist drwxrwxr-x 2 daemon daemon 4096 Feb 7 13:18 .phpstorm.meta.php -rw-rw-r-- 1 daemon daemon 16002 Feb 7 13:18 phpunit.xml.dist drwxrwxr-x 14 daemon daemon 4096 Feb 7 13:18 pix drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 plagiarism -rw-rw-r-- 1 daemon daemon 1677 Feb 7 13:18 pluginfile.php drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 portfolio drwxrwxr-x 6 daemon daemon 4096 Feb 7 13:18 privacy drwxrwxr-x 12 daemon daemon 4096 Feb 7 13:18 question drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 rating -rw-rw-r-- 1 daemon daemon 1894 Feb 7 13:18 README.md drwxrwxr-x 23 daemon daemon 4096 Feb 7 13:18 report drwxrwxr-x 6 daemon daemon 4096 Feb 7 13:18 reportbuilder drwxrwxr-x 25 daemon daemon 4096 Feb 7 13:18 repository -rw-rw-r-- 1 daemon daemon 3035 Feb 7 13:18 r.php drwxrwxr-x 4 daemon daemon 4096 Feb 7 13:18 rss drwxrwxr-x 8 daemon daemon 4096 Feb 7 13:18 search -rw-rw-r-- 1 daemon daemon 670 Feb 7 13:18 security.txt -rw-rw-r-- 1 daemon daemon 67 Feb 7 13:18 .shifter.json drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 sms -rw-rw-r-- 1 daemon daemon 4940 Feb 7 13:18 .stylelintrc drwxrwxr-x 5 daemon daemon 4096 Feb 7 13:18 tag drwxrwxr-x 6 daemon daemon 4096 Feb 10 03:38 theme -rw-rw-r-- 1 daemon daemon 1667 Feb 7 13:18 tokenpluginfile.php -rw-rw-r-- 1 daemon daemon 3367 Feb 7 13:18 TRADEMARK.txt drwxrwxr-x 2 daemon daemon 4096 Feb 7 13:18 .upgradenotes -rw-rw-r-- 1 daemon daemon 71995 Feb 7 13:18 UPGRADING.md drwxrwxr-x 9 daemon daemon 4096 Feb 7 13:18 user drwxrwxr-x 2 daemon daemon 4096 Feb 7 13:18 userpix -rw-rw-r-- 1 daemon daemon 1639 Feb 7 13:18 version.php drwxrwxr-x 7 daemon daemon 4096 Feb 7 13:18 webservice

Moodle data directory permissions

Are the following permissions correct or incorrect for my Moodle data directory?:

ls -la moodledata total 6068 drwxrwxrwx 13 daemon root 4096 Mar 19 22:06 . drwxr-xr-x 6 barkingb barkingb 4096 Mar 20 21:54 .. drwxrwxrwx 2 daemon root 4096 Jan 25 2023 antivirus_quarantine drwxrwxrwx 3 daemon root 4096 Mar 20 22:28 cache drwxrwxrwx 258 daemon root 4096 Jan 25 2023 filedir -rwxrwxrwx 1 daemon root 128 Jan 16 2023 .htaccess drwxrwxrwx 2 daemon root 4096 Jan 24 2023 lang drwxrwxrwx 2 daemon root 4096 Mar 20 22:28 localcache drwxrwxrwx 6 daemon root 4096 Jan 24 2023 models -rw-r--r-- 1 daemon daemon 6143850 Mar 20 21:49 moodle-cron.log drwxrwxrwx 2 daemon root 4096 Mar 20 22:20 muc drwxrwxr-x 3 daemon daemon 4096 Oct 9 13:49 secret drwxrwxrwx 2 daemon root 12288 Mar 20 21:25 sessions drwxrwxrwx 4 daemon root 4096 Mar 20 16:10 temp drwxrwxr-x 2 daemon daemon 4096 Mar 19 22:06 trashdir

I moved my backup back into the stated directory and it STILL gives the same print!

What has happened? Where did I go wrong?

Thanks.

Average of ratings: -

Re: Caprover upgrade fail

by Howard Miller - Friday, 21 March 2025, 2:56 PM

For Bitnami support, you'll need to speak to Bitnami. Or a Bitnami forum.

We can only really provide support for Moodle and we have no idea how Bitnami packaged it up. This is why we generally do not recommend these type of installers.

Average of ratings: -

Re: Caprover upgrade fail

by Barking Bandicoot - Friday, 21 March 2025, 11:08 PM

Or a Bitnami forum.

Thanks, I have posted the issue there.

do not recommend these type of installers.

Well, I saw no warning regarding this. If I had known before hand I would have chosen differently. I now have too many services running with Caprover/docker to change unfortunately.

I will add to this post just in case a user can assist.

I ran the php upgrade.php upgrade script

This printed:

Fatal error: $CFG->dataroot is not configured properly, directory does not exist or is not accessible! Exiting.

I tired different permissions on the data folder:

sudo chown -R daemon:daemon /srv/moodle/moodledata

chown -R www-data:www-data /srv/moodle/moodledata

I also tired:

chmod -R 755 /srv/moodle/moodledata

chmod -R 755 /srv/moodle/moodledata

None of this worked.

In the config.php file

$CFG->dataroot = '/bitnami/moodledata';

is linked to /srv/moodle/moodledata

in the Caprover/Docker settings.

I changed the path to point directly to /srv/moodle/moodledata

This printed:

php upgrade.php
!!! <p>Error: database driver problem detected</p>

<p>The site administrator should verify server configuration</p><p>PHP has not been properly configured with the MySQLi extension for it to c

ommunicate with MySQL. Please check your php.ini file or recompile PHP.</p> !!!

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Re: Caprover upgrade fail

by Howard Miller - Friday, 21 March 2025, 11:22 PM

From the installation instructions: "IMPORTANT: While there are now a number of places you can get the Moodle code (including host provided Moodle installers), you are strongly advised to only obtain Moodle from moodle.org. If you run into problems it will be a great deal easier to support you.". I know, nobody reads the instructions

I think you probably fixed the dataroot problem by changing the setting. You now have a second, unrelated problem.

It means what it says. The PHP in your docker instance is missing the MySQLi extension. Again, as this is Bitnami, I have no idea how to fix that. It won't be anything to do with php.ini, though (Windows thing)

Average of ratings: Useful (1)

Re: Caprover upgrade fail

by Barking Bandicoot - Tuesday, 25 March 2025, 10:47 AM

Bitnami's first and good practice instruction is to
sudo mv /bitnami/moodle /bitnami/moodle.backup
check ✅
or did I?
Looking through the moodle files in terminal I notice in my moodle.backup directory there was another directory within it labeled moodle. huh? Odd! I do not remember it being part of the structure. Indeed the newer moodle directory did not contain it. Looking into it I see the whole moodle directory repeated. Oh!!
What I must have done is:
sudo mv /bitnami/moodle /bitnami/moodle.backup/
I backed up my moodle directory within an already existing moodle.backup -rather than over-writing it!
When I copied over files I did so from an older backup thinking it was the existing backup!
I now went into the real backup and copied over the files - and have the site back online!!
What is curious though it that I am now on version 4.5.2. Curious because I swear I was on version 4.5.1 and downloaded version 4.5.3 to upgrade to! 🤷🏻‍♂

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Re: Caprover upgrade fail

by Ken Task - Tuesday, 25 March 2025, 12:34 PM

Am not a Bitnami user. For what it's worth:

"Bitnami's first and good practice instruction is to ..."

If you go Bitnami, go Bitnami 100% ... use Bitnami Docs

https://docs.bitnami.com/

and Bitnami Forums.

Don't mix Moodle Forums with Bitnami Forums/Support ... that's a 'mistak' (nope, spelled it correctly).

Thank goodness Bitnami is just the stack and not the entire OS/Distro for this "What I must have done is ..." can be verified with a shell command:

history [enter]

"What is curious though it that I am now on version 4.5.2. Curious because I swear I was on version 4.5.1 and downloaded version 4.5.3 to upgrade to!"

Moodle has no auto upgrade nor down grade. So BTU&KB. Bitnami is 100% command line, so once again:

history [enter]

and

https://docs.bitnami.com/aws/apps/moodle/administration/upgrade/

May not be in Bitnami docs, but ... to find out exact version of core you to have:

cd /path/to/moodlecode/

fgrep '$release' version.php

There are other moodle scripts in code/admin/cli/ that should be used to check before upgrading.

cron.php, checks.php, check_database_schema.php, mysql_collation.php, scheduled_task.php, and uninstall_plugins.php

And to actually perform an upgrade .... upgrade.php

Any of those mentioned in Bitnami Docs?

https://docs.moodle.org/405/en/Administration_via_command_line

And, last but not least, by far the best way to install, update/maintain, and upgrade a moodle code base is using git versioning.

https://docs.moodle.org/405/en/Git_for_Administrators

'SoS', Ken

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Re: Caprover upgrade fail

by Howard Miller - Tuesday, 25 March 2025, 3:05 PM

You kind of ignored what I said.

Moodle is (sort of) working but the PHP install in your Docker instance is missing a vital extension. This is NOT a Moodle issue. What you do with the Moodle code won't make any difference.

Average of ratings: -

Re: Caprover upgrade fail

by Barking Bandicoot - Tuesday, 25 March 2025, 9:44 PM

Thank you Ken and Howard
Yes, yes, "it is a Bitnami issue" - acknowledged!!
I opened a bitnami github bug.

As I have already started this thread I thought it best to supply the resolution rather than leaving it hanging. That is, if this thread is irrelevantly clutering the Moodle content then there are two choices that are best; add resolution or delete.
Please delete this thread to unclutter the forums. I will see if I have the power to do so, but probably cannot.

"Moodle is (sort of) working but the PHP install in your Docker instance is missing a vital extension. This is NOT a Moodle issue. What you do with the Moodle code won't make any difference."
- I acknowledge your contribution and looked into this. It does not seem to have been an issue. The old extensions (due to Bitnami??) held up the upgrade. No php command would work. They all resulted in: Fatal error: $CFG->dataroot is not configured properly, directory does not exist or is not accessible! Exiting.

"Moodle has no auto upgrade nor down grade"
- The upgrade (manual unpack) was obtained from the official Moodle packages - https://download.moodle.org/releases/latest/
I say curious at it was Moodle 4.5.3+ that I downloaded from https://download.moodle.org/releases/latest/

Again my intention of continuing here was to tie up a loose thread in good will - not to bring in more unrelated crud to the forum.
Please delete this thread if you have to power to do so.
Thanks Ken and Howard.

Average of ratings: Useful (1)

Re: Caprover upgrade fail

by Howard Miller - Tuesday, 25 March 2025, 10:48 PM

Ok - I missed that. I might have been clearer to say "I found the problem" or similar. It really is appreciated, as many people just vanish without tell us what the resolution was.

We certainly don't remove forum posts. There's no such thing as clutter. It very well might help somebody else.

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