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https://issues.apache.org/jira/browse/PDFBOX-5689?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Tilman Hausherr resolved PDFBOX-5689.
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    Fix Version/s: 3.0.1 PDFBox
                   4.0.0
         Assignee: Tilman Hausherr
       Resolution: Fixed

This warning is related to advanced features that most people never use 
(substitutions / ligatures). It's unclear if this is a minor error in the font 
or a programming error. I've moved it t debug so in the next version it won't 
bother you.

> Many new warnings "newGlyph ... newValue: ... is trying to override the 
> oldValue" after upgrade to V3.0.0
> ---------------------------------------------------------------------------------------------------------
>
>                 Key: PDFBOX-5689
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-5689
>             Project: PDFBox
>          Issue Type: Bug
>          Components: FontBox
>    Affects Versions: 3.0.0 PDFBox
>            Reporter: Jorge moraleda
>            Assignee: Tilman Hausherr
>            Priority: Minor
>             Fix For: 3.0.1 PDFBox, 4.0.0
>
>
> I upgraded a maven project from PDFBox 2.x to 3.0.0. I am running Linux 
> Debian stable up to date.
> Now on initialization, many (hundreds, thousands?) warnings lines appear of 
> the form:
> {{o.a.f.t.g.GlyphSubstitutionDataExtractor : For the newGlyph: 573, newValue: 
> [556, 600, 563] is trying to override the oldValue: 573}}
> The actual numbers are different in each warning.
> The severity is low, since the application still works, but I wonder if 
> thousands of these warnings is really a desirable behavior. I assume the 
> problem is with some font(s) I have installed in my system but even so, the 
> warnings did not appear on PDFBox 2.x.



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