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I have run my theme through WordPress theme checker to see if it can be submitted to WordPress.org. I encountered this error:

REQUIRED: Could not find wp_link_pages. See: wp_link_pages

But this is not true. I am using a custom function wp_my_own_link_pages() which is a replacement for wp_link_pages(). It generates pagination with a compatible HTML structure for the theme.

Did I miss something required? How can I make this work?

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The error is generated because you're not using the wp_link_pages() function in your code. The standards require that you do –  bungeshea Jan 18 '13 at 2:49
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First, this question should be asked on the Theme Reviewers mail-list, not at WPSE. If you want official answers, you should use the official communication channels.

But to answer your question in brief: Themes that implement core features/functionality are required to support the core implementation of those features/functionality.

Thus, the requirement to use wp_link_pages() is... a requirement. Note that if you need to modify the HTML markup of the generated pagination links, you can use the arguments passed to wp_link_pages().

Functions that are filterable can have filters applied, but wholesale replacement of core functions does not conform to the Guidelines.

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It should be okay. The requirement exists to make sure page pagination works. If it does you are fine. Note the theme checker cannot test all requirements, even much simpler cases will fall through.

That’s why there is a theme review team, where humans make the real tests. If your upload fails, ask on the mailing list theme-reviewers.

Update: As Chip said it is a literal requirement. Unfortunately, wp_link_pages() has not enough filters to be really useful, so you have to submit a simplified version of your theme to wordpress.org. But you can offer an advanced version on the page for your theme.

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Thanks Toscho, that's very enlightening. –  Codex Meridian Jan 18 '13 at 1:12
    
It's actually not okay. WPORG-hosted Themes are required to support core implementation of any features a Theme integrates. That means using core functions, rather than custom-defined functions that do the same thing. –  Chip Bennett Jan 18 '13 at 1:30
    
Note: this is a known issue. There are several tickets open regarding improving wp_link_pages(), including #13578, #21002, and #21266. The general philosophy of the Theme Review Team is to drive improvements back upstream into core via Trac tickets/patches, rather than facilitating ad-hoc work-arounds on a per-Theme basis. –  Chip Bennett Jan 18 '13 at 2:00
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@ChipBennett Unless these tickets are resolved theme authors should not be forced to submit a “dumbed down” version to the repository. Quite the contrary: showing what is possible and needed could help fixing the bugs. –  toscho Jan 18 '13 at 2:03
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Thanks Chip Bennett, but if I have a perfectly working function is there a simple way to make it pass by the theme checker without complicating things? –  Codex Meridian Jan 18 '13 at 5:23
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