This is likely fixed in a newer release, by this commit:
http://cgit.freedesktop.org/xorg/util/lndir/commit/?id=a0ddf1288b3fc6cf628f1ee69b585615387b5b1a
** Changed in: xutils-dev (Ubuntu)
Status: Confirmed => Fix Released
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https://bugs.launchpad.net/bugs/546571
Title:
lndir can't link files > 2gB in 10.4 beta
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