I see this with 4.6 and 4.6.1.alpha0
drkir...@hawk:~/sage-4.6$ grep WARN docpdf.log
writing... /export/home/drkirkby/sage-4.6/devel/sage/doc/en/faq/faq-usage.rst::
WARNING: unusable reference target found: about:plugins
writing...
/export/home/drkirkby/sage-4.6/devel/sage/doc/en/tutorial/introduction.rst::
WARNING: unusable reference target found: ../installation/index.html
/export/home/drkirkby/sage-4.6/devel/sage/doc/en/tutorial/sagetex.rst:: WARNING:
unusable reference target found: ../installation/index.html
writing...
/export/home/drkirkby/sage-4.6/devel/sage/doc/en/reference/other/sagetex.rst::
WARNING: unusable reference target found: ../../installation/index.html
writing...
/export/home/drkirkby/sage-4.6/devel/sage/doc/fr/tutorial/introduction.rst::
WARNING: unusable reference target found: ../../en/installation/index.html
/export/home/drkirkby/sage-4.6/devel/sage/doc/fr/tutorial/sagetex.rst:: WARNING:
unusable reference target found: ../../en/installation/index.html
writing... /export/home/drkirkby/sage-4.6/devel/sage/doc/en/faq/faq-usage.rst::
WARNING: unusable reference target found: about:plugins
writing...
/export/home/drkirkby/sage-4.6/devel/sage/doc/en/tutorial/introduction.rst::
WARNING: unusable reference target found: ../installation/index.html
/export/home/drkirkby/sage-4.6/devel/sage/doc/en/tutorial/sagetex.rst:: WARNING:
unusable reference target found: ../installation/index.html
writing...
/export/home/drkirkby/sage-4.6/devel/sage/doc/en/reference/other/sagetex.rst::
WARNING: unusable reference target found: ../../installation/index.html
writing...
/export/home/drkirkby/sage-4.6/devel/sage/doc/fr/tutorial/introduction.rst::
WARNING: unusable reference target found: ../../en/installation/index.html
/export/home/drkirkby/sage-4.6/devel/sage/doc/fr/tutorial/sagetex.rst:: WARNING:
unusable reference target found: ../../en/installation/index.html
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