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Now, so many packages for Linux are ".bin" files. However, on my Fedora Core 5 OS, it says that bin files I download and attempt to install are harmful to my system. Are they harmful to my system, and if not, how can I get Linux to accept them?
First of all, bin is a shortcut for binary, which is base 2 math counting and computer code (01010101101...)
.bin won't harm your computer, but if you'll make a mistake while installing, bin files are harmfull just as any other file type.
They are only harmful in that they install through means other than RPM, the package manager. They may also be harmful because of the strange paths that Fedora likes putting things, but that is not really a problem with the BIN. You can install and use the "checkinstall" program to convert the BIN into a RPM and install it.
Bin files are generally safe to install. Some distros will issue a warning when you try to install such files, but its just to make sure that you are aware that you could be install something potentially dangerous.