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W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
W: Target Translations (main/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list:1 and /etc/apt/sources.list.d/patches.list:1
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Actually these error messages tell you pretty much the problem: there are some source repositories that are defined twice, in the files /etc/apt/sources.list.d/elementary-os-ubuntu-os-patches-xenial.list and /etc/apt/sources.list.d/patches.list.

You should look for the lines that appear in both of the files and delete them in one of them.

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