If your Sage build is incomplete, some packages have been built, say,
pari, and then you decide to replace pari
with a system package then you need to uninstall it.
In your config.log there is

configure:38410: result: pari-2.11.4.p0:
already installed as an SPKG

e.g. for pari you'd need to run

make pari-clean

The easiest is to clean everything already built  by running

make distclean

and then start again, by running ./configure
If it is happy about system's pari,  you will see

configure:38410: result: pari-2.11.4.p0:
using system package; SPKG will not be installed

in the output of ./configure (and in config.log)

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