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I have installed Drupal Commerce 2 through composer as mentioned in

https://docs.drupalcommerce.org/commerce2/developer-guide/install-update/installation

after that, I have installed a few modules and a Barrio (Theme) directly through drupal admin interface.

Can I still update them through composer?

I have tried to update with ~/composer.phar update drupal/block_class --with-dependencies, but I am getting the following output.

DrupalProject\composer\ScriptHandler::checkComposerVersion Package "drupal/block_class" listed for update is not installed. Ignoring.
Loading composer repositor
Updating dependencies (including require-dev)
Nothing to install or update
Generating autoload files
DrupalProject\composer\ScriptHandler::createRequiredFiles

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Can I still update them through composer?

No, Composer can only manage packages that have been installed through Composer.

You could always add it to the "require" section of your existing composer.json (manually or by executing composer require), then Composer will know about it.

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