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For example, say mypackage-9.1.tgz contained /packages/mypackage/foo/file, /packages/mypackage/foo/file2, and /packages/mypackage/foo/file3. I then add /packages/mypackage/foo/file4. If I then upgradepkg mypackage-10.0.tgz (a package that also contains various files in /packages/mypackage/foo), what will happen to file4?
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If mypackage-10.0.tgz DOES NOT include /packages/mypackage/foo/file4, then /packages/mypackage/foo/file4 is left alone. If mypackage-10.0.tgz DOES include /packages/mypackage/foo/file4, then /packages/mypackage/foo/file4 is replaced with /packages/mypackage/foo/file4 from mypackage-10.0.tgz.
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What if I changed file3 and mypackage-10.0.tgz also contains a file3?
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The pre-existing file3 will be replaced by the file3 from mypackage-10.0.tgz.
Note that this is all generically speaking. There is an exception to this if the files are configuration files. In that case, it is assumed that you do not wish to blow away your current configuration, so the original file is left in place and the new configuration file has a ".new" extension appended to it's name.
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What will upgradepkg do if software was installed either through make install
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If a package was installed via "make install" it is not recognized by the Slackware package management system. "upgradepkg" alone will only give you an error. "upgradepkg --install-new" will install the new package, overwriting pre-existing files. It can have issues, though, in that it will not remove any files included in the older version that are no longer a part of the package being installed.
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or by checkinstall but with a name that doesn't exactly match the Slack format
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Basically, the same thing as above. You can simply "removepkg" the older package with the alternate name and you will be all set. No such luxury if you used only "make install."
Note that if you didn't install your self-compiled stuff with the same configure options that the Slackware packages use, you will most definately have orphaned files (or you could look at it as having two versions of the same software installed concurrently). If this is the case, "which" will be your friend.