Update how catmaid.server is read

[mmc46]

Functions such as check_duplicate_synapses() use simple_catmaid_url() to get the URL of the CATMAID server, with getOption("catmaid.server") to build URLs, for example. This relies on having this set in .Rprofile.

As these settings should now live in .Renviron, catmaid_login()$server should be used instead.

[SridharJagannathan]

Hi @mmc46 Thanks for this, Can you please post a minimal working example reproducing the bug, so when closing this issue those test cases can be run.

[mmc46]

check = check_duplicate_synapses(skid = 27295)
check$URL_1
[1] "?pid=1&xp=365832&yp=158573&zp=156200&tool=tracingtool&active_skeleton_id=27295&active_node_id=6526212&sid0=5&s0=0"
[2] "?pid=1&xp=362479&yp=160894&zp=150720&tool=tracingtool&active_skeleton_id=27295&active_node_id=6883999&sid0=5&s0=0"

URL is missing the CATMAID server.

catmaid::catmaid_login()$server
[1] "https://neuropil.janelia.org/tracing/fafb/v14"