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Using alien, I can convert RPM format package into .deb package.

The question is, which is the best way to handle RPM format package in Ubuntu/Debian? Should I use alien to convert it to .deb and install using dpkg, or install RPM and use it to install the the RPM format package?

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Alien is the system to use. As the Debian rpm package description states:

If you want to install Red Hat Packages then please use the alien package. Using rpm directly will bypass the Debian packaging system!

Typically, you do not want that. If at all possible, I recommend rebuilding the software from source for a Debian system. Alien will simply move files around, add scripts and change the archive to be dpkg compatible. It will not fix executables linked to non-existant or wrongly-versioned libraries.

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My opinion is to keep all packages in a single system; by using Alien to convert the package you can still work with it via apt/aptitute/synaptic.

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