[MacPorts] #45401: Pymol destroot fails

[MacPorts]

#45401: Pymol destroot fails
----------------------------+--------------------------------
 Reporter:  josh.baraban@…  |      Owner:  macports-tickets@…
     Type:  defect          |     Status:  new
 Priority:  Normal          |  Milestone:
Component:  ports           |    Version:  2.3.1
 Keywords:                  |       Port:  pymol
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 The pymol destroot stage fails, apparently because it creates a file in
 the destroot directory and then attempts to copy over it.

 Error: org.macports.destroot for port pymol returned: error copying
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_pymol/pymol/work/pymol/setup/pymol_macports"
 to
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_pymol/pymol/work/destroot/opt/local/bin/pymol":
 file already exists

 I tried cleaning, and also deleting the offending file manually, but the
 destroot stage of the port, which I ran individually, creates it and then
 throws an error because of it.

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Ticket URL: <https://trac.macports.org/ticket/45401>
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