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Using the simple npm deprecate command you can deprecate versions of published packages. This only works if you are the owner of the specified package.
npm deprecate jQuery "This is deprecated"
Keep in mind that a message must be also specified after the package name/version.
Version ranges can also be specified:
npm deprecate jQuery@"<0.1.2" "Bug fixed"
This will deprecate every version that is smaller than 0.1.2 of the specified package (jQuery in this case).
Packages can also be un-deprecated by specifying an empty string as the message: