R – best compression algorithm with the following features

It sounds like what you're trying to do is work out a large number of compression possibilities for every possible segment (let's call your variable length 1-64K blocks segments) of the file. Correct me if I'm wrong, but are you working out the best compression for the first segment from the following choices (method 0 is uncompressed):

• compression method 0, length 1 byte.
• compression method 1, length 1 byte.
• : : : : :
• compression method 6, length 1 byte.
• compression method 0, length 2 bytes.
• compression method 1, length 2 bytes.
• : : : : :
• compression method 6, length 65534 bytes.
• compression method 0, length 65535 bytes.
• compression method 1, length 65535 bytes.
• compression method 2, length 65535 bytes.
• compression method 3, length 65535 bytes.
• compression method 4, length 65535 bytes.
• compression method 5, length 65535 bytes.
• compression method 6, length 65535 bytes.

That's going to take a huge amount of time (roughly 420,000 compression attempts per segment). If that is what you're doing, you'll be better off choosing a single segment size (e.g., 64K) and applying each of the seven compression methods to it to choose the best. Then, for each segment, output the "method" byte followed by the compressed data.