The Clock strikes one that just struck two — The Comedy of Errors

Dromio of Syracuse: "No, no, the bell, it's time that I were gone: It was two ere I left him, and now the clock strikes one." ─ The Comedy of Errors

This poem talks about the Great Schism of the West, a rivalry within the Christian world. The key is to solve the "Vagabond for Genesis."

The word Vagabond appears four times in Bible, two in Genesis both indicating Cane who killed his brother. Brother is a fellow-member of a Christian society, so a vagabond for Genesis infers a Christian who attacks another Christian. The answer is then hinted by schism in line two.

The Clock strikes one that just struck two－
Some schism in the Sum－
A Vagabond for Genesis
Has wrecked the Pendulum－
(F.1598/J.1569)
[1] Clock:: the bell of a church. strike:: to impel, urge. one:: one belief. struck two:: split to two.
[2] Schism:: the Great Schism, a division of the Christian world for fifty years from the end of the 14th century. Sum:: summary, epitome (OED n.1 9a).
[3] Vagabond, Genesis:: Cain is called a "vagabond" in Genesis for he slew his brother; brother is "a fellow-member of a Christian society" (OED 3).
[4] wrecked the Pendulum:: the regular working pattern of the Christian world was wrecked.

When thou tillest the ground, it shall not henceforth yield unto thee her strength; a fugitive and a vagabond shalt thou be in the earth. And Cain said unto the LORD, My punishment is greater than I can bear. (Genesis 4:12-13)

This danger had passed like a thousand others before, and the Church still stood in unimpaired vigor. Next came the Great Schism of the West, which lasted for nearly forty years, at the end of the fourteenth and the beginning of the fifteenth century. It was occasioned by the return of the Popes from Avignon to Home in 1378, and it was perpetuated by the French cardinals, who were encouraged by the French court. ─ The History of the Protestant Reformation (1860)

Great Schism in the Church of Rome. During the heresy of Wickiliffe, the Christian church was afflicted with schism, originating from the ambition of some of the cardinals, and the loose conduct of others, which pope Urban VI. was desirous of reforming. ─ Review of Fox's Book of Martyrs (1826)