Hello all,
In Spring 2018 I was working on packaging interpro-scan for some work. There were a number of packages which has some build or test failures which I worked on. Of these, Hmmer needed some more attention. Originally, this was an upstream request to tweak their autoconf but that went bizarrely bad. At that point, I went in to fix up a decade's worth of technical debt. Of these were removal of Parallel Virtual Machine support, adjusting buffer sizes upwards for memory found on modern systems, hard code enabling of pthreads, renaming executable to hmmer2 in the build to not conflict with hmmer or hmmer3 to allow for parallel installation, and simplification of the configuration header. All unit tests pass. There is a need for parallel installation of hmmer2 and hmmer3 because hmmer2 works on a global genome scale, while hmmer3 is build to only operate on parts of the genome.
This should have do change in behavior or output in any way except for removal of PVM support and minor runtime changes. This change set should be viewed strictly as a technical debt clean up.