richardsc
commented
3 years ago I can comment on why those warnings exist. Because there is no consistent standard for variable names and units in ODF files, we have coded oce to be able to recognize (and convert to something sensible) the most common ones. Instead of choking on unknown ones, we just leave it as it, and spit a warning.
Catching all the different variables, and units, is a game of whack-a-mole for basically all format types (even SeaBird CNV files).
Here are the warnings/errors that the OCE package outputs when I am converting the ODF files to JSON. There are 27 test files in the repo currently and only 3 have warnings. Not sure if this is even a problem but I'm putting it here if anyone feels like investigating
../sample_data/mli_data/2020-12-23/ODF_files_MLI/PLNKG_2019004_1_1_Z.ODF R[write to console]: Error in names(NAvalueList) <- namesUnits$names : 'names' attribute [16] must be the same length as the vector [9]
R[write to console]: In addition: R[write to console]: Warning messages:
R[write to console]: 1: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[9]='microns', for item named 'MNSZ', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 2: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[10]='microns', for item named 'MXSZ', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 3: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[14]='g', for item named 'WTWT', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 4: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[15]='g', for item named 'DRWT', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
Error in names(NAvalueList) <- namesUnits$names : 'names' attribute [16] must be the same length as the vector [9]
../sample_data/mli_data/2020-12-23/ODF_files_MLI/PLNKG_2019004_201_1_P.ODF R[write to console]: Error in names(NAvalueList) <- namesUnits$names : 'names' attribute [12] must be the same length as the vector [6]
Error in names(NAvalueList) <- namesUnits$names : 'names' attribute [12] must be the same length as the vector [6]
test_files/CTD_1994038_147_1_DN.ODF R[write to console]: Warning messages:
R[write to console]: 1: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[4]='deg C', for item named 'temperature', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 2: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[6]='deg C', for item named 'temperature2', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 3: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[14]='mmol/m^3', for item named 'NTRA', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 4: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[17]='µeinsteins/s/m^2', for item named 'SPAR', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 5: R[write to console]: In ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER = NULL, : R[write to console]:
R[write to console]: unable to interpret ODFunits[22]='µM', for item named 'OXYM', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string
R[write to console]: 6: R[write to console]: In (function (file, columns = NULL, header = "list", exclude = NULL, : R[write to console]:
R[write to console]: estimating waterDepth from maximum pressure
R[write to console]: 7: R[write to console]: In (function (file, columns = NULL, header = "list", exclude = NULL, : R[write to console]:
R[write to console]: estimating waterDepth from maximum pressure
R[write to console]: 8: R[write to console]: In (function (file, columns = NULL, header = "list", exclude = NULL, : R[write to console]:
R[write to console]: estimating waterDepth from maximum pressure