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I want to install a set of software organized into directories at the root level.

Is there any method in which I can use pacman to install certain packages into a directory of my choosing?

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Yes, that's possible, by specifying a different root location,

-r, --root Specify an alternative installation root (default is /). This should not be used as a way to install software into /usr/local instead of /usr. This option is used if you want to install a package on a temporary mounted partition that is "owned" by another system. NOTE: if database path or logfile are not specified on either the command line or in pacman.conf(5), their default location will be inside this root path.

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What should I do about the dbpath with that method? – Terry Chia Oct 2 '12 at 9:46
@TerryChia you want to alternate where pacman stores information of installed packages? – warl0ck Oct 2 '12 at 9:52
No, but I got an error: failed to initialize alpm library (could not find or read directory), which from some googling - i assume to be an error with the dbpath. – Terry Chia Oct 2 '12 at 9:56
@TerryChia Hmm, I think the '-r' is used to install a new system just like what the Installation Media does, I don't have a Arch at hand right now, will try it later. If this doesn't work, you're going to modify the PKGBUILD file, the XXX_install function defined there. (A prefix can be specified for most software based on autogen) – warl0ck Oct 3 '12 at 10:06

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