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Using AP_VENDOR_PUB_PKG create_vendor or create_vendor_site, you will NOT be able to update the PAYMENT METHOD in R12.
AP_VENDOR_PUB_PKG create_vendor or create_vendor_site packages are obsolete in R12 and we shouldn't be using the same. Instead use the supplier open interface table to import the suppliers and supplier sites.
In R12 PAYMENT_METHOD_LOOKUP_CODE column is replaced by PAYMENT_METHOD_CODE. In R12 the column PAYMENT_METHOD_LOOKUP_CODE is no longer used.
When I was upgrading I had the same issue and when I crated the SR with Oracle they suggested me to use the Supplier open interface tables, which resolved my issue.
Hope this helps.