Bit Rot

The idea of “bit rot” might seem a bit fanciful. After all, perishable things like autumn leaves rot, but why should a substance as intangible as software undergo something similar? We were recently asked by a colleague for an executable of the program alfy we had published back in 2011. She hoped to used alfy to detect recombination among genomes of the bacterium Pseudomonas fluorescens and its relatives. We thought that should be easy, but running make in the directory of alfy’s C sources only produced a long list of warnings that ended in an error. Clearly something was rotten in the state of that software. It took a while to remove the rot, but in this repo alfy is now back to where it was in 2011.