If a package is only supplied in autopackage format, you must not add it to the tree. If a package is supplied in autopackage format and some other sane standard format (for example a source tarball), use the other format only.
Autopackage packages are totally unsuitable for Gentoo systems for a large number of reasons:
- To even unpack the package, you must run arbitrary code supplied by an untrusted source.
- They install directly to the live filesystem.
- Their intrinsic dependency resolver is broken.
- They do not support the filesystem layout used by Gentoo.
- They do not support configuration protection.
- They can clobber arbitrary files on uninstall.
- The linking mechanism used is insufficiently flexible.
- The entire format is completely unportable and highly tied to x86 Linux systems.
Upstream are aware of these issues and have no desire to fix them — indeed, they pass off some of their most broken behaviour as 'features'.