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I think the issue that Jon is referring to is that many maintainers are adamant in sticking to certain versions of libraries that calibre uses, resulting in builds that are quite often crippled or broken in some subtle manner.
One issue I found yesterday on trying the flatpack version on my chromebook yesterday is that when I ran calibre in debug mode, I was told the log file was being written to /tmp/{some file name}, which did not exist.
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