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I have a machine that does not have an internet connection and I need to download a few packages to it.

I can use apt-get download xxx to get the package, but, if I ever connect this machine to the internet, will apt-get update / upgrade know what this package is and update it successfully, or will it cause problems in the future?

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Assuming you use apt-get download to download the packages, copy them to the "isolated" machine and install with sudo dpkg -i *.deb (or similar), then yes, apt-get will know that these packages/versions have been installed and will upgrade them if necessary.

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It depends on the type of Package installation you do. If you install packages VIA officially provided .deb package then you don't have to worry .

sudo apt-get update && sudo apt-get upgrade will work flawlessly , even if you are doing an offline update and connect it to Internet sometime later , it will work.

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All required info of a package are located in the package (like name and version). When you need to update, it is basically comparing the vesrion of the package you have installed and the version of the package in the repositories. So in short, apt-get update and apt-get upgrade will upgrade the package as long as the package is in the repositories installed on the second machine.

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I'm not sure I understand "as long as the package is in the repositories installed on the machine". Could you clarify? – John S Gruber Aug 13 '12 at 15:56
@JohnSGruber For example, if you added a repository with add-apt-repository, and downloaded a package that exists in it, and not in the official repository, you won't be able to upgrade the package on the second machine unless you add the repository on that machine too. – Dan Aug 13 '12 at 16:15

In cases where .deb files are not available you can also download the source and build it yourself. That would work fine too.

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But that could cause the package confusion later when the package is installed with apt-get. – John S Gruber Aug 13 '12 at 15:57

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