I found that for some reason berkeleydb refuses to use pthreads installed on the gumstix. I've tried building the db with test and set by supplying "ARM/gcc-assembly". Also, I had to add -fPIC to CFLAGS to get it dtnd to load it on the verdex board. Lastly, it appears that the dtn build compiles in absolute paths, which has its issues since now it looks for the tcl in /home/timur/.... I ended up adding a symlink to the build. I will add more here once I make more progress.
Ok, Berkeley DB seems to be running with test-and-set, but now dtn crashes at the assertion: ASSERTION FAILED ((u_int)now.tv_sec >= TIMEVAL_CONVERSION) at bundling/BundleTimestamp.cc:39. I tried adding printf in there to see the value of now.tv_sec and I tried printing it to a file, but neither way produced any output (I did replace the dtnd file after recompiling). I'm not sure what the issue is and how to go about resolving it. I will look into this more tomorrow. I'm hoping Brian will know something about this, but not keeping my hopes up. If I can figure out why nothing is printed it'd be a big step in troubleshooting.
EDIT: Ok, the problem is not with the code or the assertion. DTN checks if the time is past midnight UTC December 31st, 1999 is (probably to make sure packet dates can be used correctly). The gumstix were set to midnight December 31st, 1969, thus the assertion was failing. I have DTN now running on the gumstix.