configure:3020: /usr/pkgsrc/wip/avr-gcc/work/obj/./gcc/xgcc
-B/usr/pkgsrc/wip/avr-gcc/work/obj/./gcc/ -B/usr/pkg/avr/bin/
-B/usr/pkg/avr/lib/ -isystem /usr/pkg/avr/include -isystem
/usr/pkg/avr/sys-include -o conftest -g -I/usr/pkg/include conftest.c  >&5
exec: : permission denied

configure:3020: /usr/pkgsrc/wip/avr-gcc/work/obj/./gcc/xgcc -B/usr/pkgsrc/wip/avr-gcc/work/obj/./gcc/ -B/usr/pkg/avr/bin/ -B/usr/pkg/avr/
lib/ -isystem /usr/pkg/avr/include -isystem /usr/pkg/avr/sys-include    -o conftest -g -I/usr/pkg/include   conftest.c  >&5
exec: : permission denied
configure:3023: $? = 1
configure:3211: checking for suffix of object files
configure:3233: /usr/pkgsrc/wip/avr-gcc/work/obj/./gcc/xgcc -B/usr/pkgsrc/wip/avr-gcc/work/obj/./gcc/ -B/usr/pkg/avr/bin/ -B/usr/pkg/avr/
lib/ -isystem /usr/pkg/avr/include -isystem /usr/pkg/avr/sys-include    -c -g -I/usr/pkg/include  conftest.c >&5
exec: : permission denied

また同じことが。もしかして 版名の同じ wip/avr-binutils-2.23.2 の古いやつか。
その通りで avr-binutils を作り直したら解決した。