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) -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq3meRpfrT9fWhZs4t7q2msxftQmj15MGwbKQJQxsDscHQ%40mail.gmail.com.