If I disable the check for duplicated references, then I get the following:
Checking non-numbered parts...
Checking nets with only one connection...
ERROR: Net 'unnamed_net412' is connected to only one pin: CONN901:2 .
ERROR: Net 'unnamed_net411' is connected to only one pin: CONN901:1 .
ERROR: Net 'unnamed_net404' is connected to only one pin: P601:65 .
ERROR: Net 'unnamed_net294' is connected to only one pin: C503:1 .
ERROR: Net 'unnamed_net254' is connected to only one pin: U402:A8 .
ERROR: Net 'unnamed_net253' is connected to only one pin: U402:B7 .
ERROR: Net 'unnamed_net246' is connected to only one pin: U402:E8 .
ERROR: Net 'unnamed_net245' is connected to only one pin: U402:F7 .
ERROR: Net 'unnamed_net191' is connected to only one pin: CONN901:2 .
ERROR: Net 'unnamed_net190' is connected to only one pin: CONN901:1 .
ERROR: Net 'unnamed_net183' is connected to only one pin: P601:65 .
ERROR: Net 'unnamed_net61' is connected to only one pin: C503:1 .
ERROR: Net 'unnamed_net21' is connected to only one pin: U402:A8 .
ERROR: Net 'unnamed_net20' is connected to only one pin: U402:B7 .
ERROR: Net 'unnamed_net13' is connected to only one pin: U402:E8 .
ERROR: Net 'unnamed_net12' is connected to only one pin: U402:F7 .
ERROR: Net 'MDQS3' is connected to only one pin: U101:A23 .
ERROR: Net 'MDQS2' is connected to only one pin: U101:B19 .
Checking pins without the 'pintype' attribute...
ERROR: Stack overflow
Is the stack that is referenced a guile stack? Is this a simple matter of guile configuration? (I don't know anything about guile...)