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I recently reinstalled emacs after some technical difficulties. I managed to keep some of my personal configuration files, which I believe may have caused an issue. As I went to install packages, I discovered that each non-installed package had a duplicate. I figure this is due to remnant from when I transferred my data over, but I am unsure as to exactly what.

zalba19
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each non-installed package had a duplicate

It's because you have multiple package repositories added to the package-archives list. It is OK for a package to be present in multiple repositories, say GNU Elpa and Melpa.

The Archive column in the Package Menu buffer indicates the archive name like gnu (GNU Elpa), melpa (Melpa), marmalade (Marmalade). You, the user, can choose which version of the package to install.

Are you sure each non-installed package has a duplicate? Or is it many of them?

On another note, if you are re-installing emacs and you already have an emacs config, it might be a good idea to remove the ~/.emacs.d/elpa directory (IF you maintain a list of all the packages you installed).

This step will get rid of all the duplicate package rows that appear with the obsolete tag (if any) that showed up in the Archive column in Package Menu buffer (M-x list-packages).

See also:

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Kaushal Modi
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    I am aware of the different repositories. These duplicates are exactly the same (same version, same repository etc.). I did remove the /elpa directory to update everything though – zalba19 Nov 06 '15 at 03:43
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    @zalba19 I have never seen that. So hopefully someone else can throw light on this issue. btw it is not clear if you still saw this issue after deleting elpa/ dir.. IMO deleting elpa/ and re-installing all packages should resolve the problem. – Kaushal Modi Nov 06 '15 at 03:47
  • Thanks for the help. I started observing the issue before deleting elpa/, but unfortunately deleting it did not fix the issue. – zalba19 Nov 06 '15 at 04:05
  • Do you see duplicate packages even in an emacs -Q session? Also what emacs version are you on? – Kaushal Modi Nov 06 '15 at 04:08
  • I am on emacs 24.5. Booting up with emacs -Q, I don't get any duplicates, so there is something going on – zalba19 Nov 06 '15 at 04:23
  • Well then, the solution is not far. Gradually keep on commenting your config in halves (1/2, 3/4, 7/8, ...), and restarting emacs at each step. At one point, you will see the problem go away and then you use the same technique recursively, but this time uncommenting that last commented section, and so on till you narrow down to the offending piece of code. Please report your findings. – Kaushal Modi Nov 06 '15 at 04:31
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    Wild guess.. When you do C-h v package-archives, do you see the same repository repeated twice by any chance. – Kaushal Modi Nov 06 '15 at 04:34
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    Why yes it did. Thank you. I imagine deleting the second one, deleting elpa/ and rerunning emacs should fix this issue. Thank you – zalba19 Nov 06 '15 at 04:40
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    Nope, just fixing your config to make sure that you don't have duplicate entries in package-archives and restarting emacs should fix it. – Kaushal Modi Nov 06 '15 at 04:43