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Can someone explain to me why people (sometimes) use "is" instead of "has" in the following example:

"The time is come."

Is it just the way people speak? Because I don't think I've ever seen anyone write it like that.

Thanks.
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It's quite possible that you're repeatedly misinterpretting a reduction of the word has.

However, people might jocularly use 'is' that way on rare occasions, possibly as a way of intentionally making the sentence sound archaic. You can also find that sort of usage in English written in the 1600s, for example.
What about this sentence:

'Where is he gone?'

I've seen people use this plenty of times. Shouldn't it be has instead of is?
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I've never heard of anyone saying the time is come. It could be that they are speaking fast and it sound like IS. I said that sentence a few times and to me it does seem like is so it's possible that's how you heard it too. Go ahead and say it 5 times fast and you'll see what I mean.
AstonishingWhat about this sentence:

'Where is he gone?'

I've seen people use this plenty of times. Shouldn't it be has instead of is?

That sounds very odd. You're quite sure that's what was being said?
I think you are hearing the abbreviated 's for 'has' and interpreting it as is.

The time's come =The time has come - but it would sound rather like the time is come.

Where's he gone? = Where has he gone - but it sounds rather like where is he gone.
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"The time is come."'

This is old/historical usage.

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When Adam delved and Eve span, Who was then the gentleman?[1] From the beginning all men by nature were created alike, and our bondage or
servitude came in by the unjust oppression of naughty men. For if God
would have had any bondmen from the beginning, he would have appointed
who should be bond, and who free.

And therefore I exhort you to consider that now the time is come,
appointed to us by God, in which ye may ( if ye will ) cast off the
yoke of bondage, and recover liberty.

http://en.wikipedia.org/wiki/John_Ball_(priest)
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Marius Hancu"The time is come."'

This is old/historical usage.

Right you are, Marius. In German sein, the German equivalent of be, is still used as a parfect and pluperfect auxiliary with certain verbs. Except for some exceptional cases, have is used in English and har in Swedish and the other Scandinavian Germanic languages. I don't know about Dutch and Flemish.

CB