I think there are two possibilities here - either the starter script gpsprune doesn't parse the proxy information properly and passes the wrong information to GpsPrune, or the networking stuff used by GpsPrune doesn't take any notice of what's passed in. It would be very useful to know whether starting GpsPrune from the command line with java -Dhttp.proxyHost= -Dhttp.proxyPort=3128 -jar /usr/share/gpsprune/gpsprune.jar
makes things behave as you want.

Looking at Debian's gpsprune script (in 10.1), I can't see any reason why it wouldn't pass the port properly through - if I give it then it appears to correctly split up the host and port, and pass both successfully onto GpsPrune. So knowing whether the direct specification works or not would help rule out the gpsprune script as the problem.

Another problem I see in this script (although I'm not too familiar with bash), is what happens when you give a host but no port? In the case of "";, it correctly identifies the host as "", but the second sed command fails to find a match, and returns the whole $http_proxy variable. So I end up with host= and port= - surely that can't be right. Perhaps it is rejected later and reset to 80 by the networking classes? But I assume that rather than checking [ -z $proxyport ], it should be running a grep and looking at the return code to see whether a match was found or not.

Any Debian bash experts feel like commenting on this one?

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