Sorry about not having read the doc, I'm probably too used to import shape
files
with readOGR() and did not realize that GPX files would have different
options.

test <-
readOGR(dsn="/media/TRANSCEND/MONTSENY2008/MONTSENY_GEODATA/FloraExotica2009/AilantMSY09R.gpx",layer="waypoints")

works fine and the table is correct. I think that 
dataset_options="GPX_USE_EXTENSIONS=YES"
at writing did the job.

So no problem at all with writing/reading GPX files in R through rgdal
I would add a line to the help page reminding the user that coordinates must
be geographic in GPX
files (thus the user must eventually unproject before writeOGR() ).

Thanks!

Agus
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