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Several warnings in CI #933

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Sbozzolo opened this issue Aug 20, 2024 · 2 comments · Fixed by #1043
Closed

Several warnings in CI #933

Sbozzolo opened this issue Aug 20, 2024 · 2 comments · Fixed by #1043
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Maintenance and I...

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@Sbozzolo
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E.g., here: https://github.com/CliMA/ClimaCoupler.jl/actions/runs/10479084890/job/29023941430?pr=932

┌ ClimaCoreTempestRemap
│  WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ CairoMakie
│  WARNING: Makie.Combined is deprecated, use Plot instead.
│    likely near none:1
│  WARNING: importing deprecated binding Makie.Combined into CairoMakie.
│  , use Plot instead.
│  WARNING: Makie.ContinuousSurface is deprecated, use VertexGrid instead.
│    likely near none:1
│  WARNING: importing deprecated binding Makie.ContinuousSurface into CairoMakie.
│  , use VertexGrid instead.
│  WARNING: Makie.DiscreteSurface is deprecated, use CellGrid instead.
│    likely near none:1
│  WARNING: importing deprecated binding Makie.DiscreteSurface into CairoMakie.
│  , use CellGrid instead.
│  
│  [pid 4409] waiting for IO to finish:
│   Handle type        uv_handle_t->data
│   timer              0x6352050->0x7f8a61952680
│  This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
└  
┌ ClimaCoupler
│  WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ ClimaUtilities → ClimaUtilitiesClimaCoreTempestRemapExt
│  WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  
┌ Plots
│  WARNING: using deprecated binding Colors.RGB1 in PlotUtils.
│  , use XRGB instead.
│  WARNING: using deprecated binding PlotUtils.RGB1 in Plots.
│  , use ColorTypes.XRGB{T} where T<:Union{AbstractFloat, FixedPointNumbers.FixedPoint{T, f} where f where T<:Integer} instead.
│  WARNING: using deprecated binding Colors.RGB4 in PlotUtils.
│  , use RGBX instead.
│  WARNING: using deprecated binding PlotUtils.RGB4 in Plots.
│  , use ColorTypes.RGBX{T} where T<:Union{AbstractFloat, FixedPointNumbers.FixedPoint{T, f} where f where T<:Integer} instead.
└  
     Testing Running tests...
 Downloading artifact: cmip_model_rmse
 Downloading artifact: precipitation_obs
 Downloading artifact: radiation_obs
WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
WARNING: Method definition slab_index(Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:8 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:5.
WARNING: using deprecated binding Colors.RGB1 in PlotUtils.
, use XRGB instead.
WARNING: PlotUtils.RGB1 is deprecated, use ColorTypes.XRGB{T} where T<:Union{AbstractFloat, FixedPointNumbers.FixedPoint{T, f} where f where T<:Integer} instead.
  likely near /home/runner/work/ClimaCoupler.jl/ClimaCoupler.jl/test/aqua.jl:5
WARNING: using deprecated binding Colors.RGB4 in PlotUtils.
, use RGBX instead.
WARNING: PlotUtils.RGB4 is deprecated, use ColorTypes.RGBX{T} where T<:Union{AbstractFloat, FixedPointNumbers.FixedPoint{T, f} where f where T<:Integer} instead.
  likely near /home/runner/work/ClimaCoupler.jl/ClimaCoupler.jl/test/aqua.jl:5
WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
WARNING: Method definition slab_index(Any, Any) in module ClimaCoreTempestRemap at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/ClimaCoreTempestRemap.jl:7 overwritten at /home/runner/.julia/packages/ClimaCoreTempestRemap/s3p3V/src/netcdf.jl:4.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
Test Summary: | Pass  Total   Time
Aqua tests    |   10     10  45.7s
Test Summary:    | Pass  Total   Time
Interfacer tests |   93     93  20.4s
┌ Warning: No dates available in input data file
└ @ ClimaCoupler.Regridder ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Regridder.jl:288
┌ Warning: No dates available in input data file
└ @ ClimaCoupler.Regridder ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Regridder.jl:288
┌ Warning: No dates available in input data file
└ @ ClimaCoupler.Regridder ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Regridder.jl:288
┌ Warning: No dates available in input data file
└ @ ClimaCoupler.Regridder ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Regridder.jl:288
Test Summary:   | Pass  Total     Time
Regridder tests |   52     52  3m26.7s
typeof(cc) = ClimaCoupler.ConservationChecker.EnergyConservationCheck
rse[end] = 0.0
typeof(cc) = ClimaCoupler.ConservationChecker.WaterConservationCheck
rse[end] = 0.0
typeof(cc) = ClimaCoupler.ConservationChecker.EnergyConservationCheck
rse[end] = 0.0
typeof(cc) = ClimaCoupler.ConservationChecker.WaterConservationCheck
rse[end] = 0.0
Test Summary:             | Pass  Total   Time
ConservationChecker tests |   32     32  13.6s
┌ Warning: Initializing with `segment_idx = 1310
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:212
┌ Warning: On 1979-02-15T00:00:01 updating file data reads: file dates = [ 1979-02-15T00:00:00 , 1979-03-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: This time period is before BC data - using file from 1979-01-16T12:00:00
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:194
┌ Warning: On 1978-11-16T00:00:00 updating file data reads: file dates = [ 1978-11-16T00:00:00 , 1978-12-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: Initializing with `segment_idx = 1307
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:212
┌ Warning: On 1978-11-16T00:00:00 updating file data reads: file dates = [ 1978-11-16T00:00:00 , 1978-12-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: On 1978-10-19T12:00:00 updating file data reads: file dates = [ 1978-10-16T12:00:00 , 1978-11-16T00:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: Initializing with `segment_idx = 1306
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:212
┌ Warning: On 1978-10-19T12:00:00 updating file data reads: file dates = [ 1978-10-16T12:00:00 , 1978-11-16T00:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: This time period is after BC data - using file from 2022-03-16T12:00:00
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:234
┌ Warning: This time period is after BC data - using file from 2022-03-16T12:00:00
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:234
┌ Warning: On 1870-02-15T00:00:00 updating file data reads: file dates = [ 1870-02-15T00:00:00 , 1870-03-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: On 1870-02-18T00:00:00 updating file data reads: file dates = [ 1870-02-15T00:00:00 , 1870-03-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: No dates available in input data file
└ @ ClimaCoupler.Regridder ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Regridder.jl:288
┌ Warning: Initializing with `segment_idx = 1310
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:212
┌ Warning: On 1979-02-15T00:00:01 updating file data reads: file dates = [ 1979-02-15T00:00:00 , 1979-03-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: This time period is before BC data - using file from 1979-01-16T12:00:00
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:194
┌ Warning: On 1978-11-16T00:00:00 updating file data reads: file dates = [ 1978-11-16T00:00:00 , 1978-12-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: Initializing with `segment_idx = 1307
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:212
┌ Warning: On 1978-11-16T00:00:00 updating file data reads: file dates = [ 1978-11-16T00:00:00 , 1978-12-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: On 1978-10-19T12:00:00 updating file data reads: file dates = [ 1978-10-16T12:00:00 , 1978-11-16T00:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: Initializing with `segment_idx = [1306](https://github.com/CliMA/ClimaCoupler.jl/actions/runs/10479084890/job/29023941430?pr=932#step:6:1309)
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:212
┌ Warning: On 1978-10-19T12:00:00 updating file data reads: file dates = [ 1978-10-16T12:00:00 , 1978-11-16T00:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: This time period is after BC data - using file from 2022-03-16T12:00:00
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:234
┌ Warning: This time period is after BC data - using file from 2022-03-16T12:00:00
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:234
┌ Warning: On 1870-02-15T00:00:00 updating file data reads: file dates = [ 1870-02-15T00:00:00 , 1870-03-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: On 1870-02-18T00:00:00 updating file data reads: file dates = [ 1870-02-15T00:00:00 , 1870-03-16T12:00:00 ]
└ @ ClimaCoupler.BCReader ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/BCReader.jl:219
┌ Warning: No dates available in input data file
└ @ ClimaCoupler.Regridder ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Regridder.jl:288
Test Summary:  | Pass  Total     Time
BCReader tests |   96     96  2m53.3s
[ Info: Setting up single-process ClimaCoupler run on device: CPUSingleThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUSingleThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUMultiThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUSingleThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUSingleThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUSingleThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUMultiThreaded.
[ Info: Setting up single-process ClimaCoupler run on device: CPUSingleThreaded.
Test Summary:   | Pass  Total  Time
Utilities tests |   12     12  0.2s
[ Info: update_firstdayofmonth! at [Dates.DateTime("1979-03-21T00:00:00")]
Test Summary:     | Pass  Total  Time
TimeManager tests |  203    203  0.6s
┌ Warning: `update_field!` is not extended for the `surface_temperature` field of Unnamed: skipping update.
└ @ ClimaCoupler.Interfacer ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Interfacer.jl:214
Test Summary:        | Pass  Total   Time
FieldExchanger tests |  100    100  10.4s
┌ Warning: Simulation Unnamed uses the default thermo (saturated) surface state
└ @ ClimaCoupler.FluxCalculator ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/FluxCalculator.jl:320
┌ Warning: Simulation Unnamed uses the default thermo (saturated) surface state
└ @ ClimaCoupler.FluxCalculator ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/FluxCalculator.jl:320
Test Summary:        | Pass  Total   Time
FluxCalculator tests |   33     33  47.6s
┌ Warning: Variable Val{:z}() is not defined.
└ @ ClimaCoupler.Diagnostics ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Diagnostics.jl:89
┌ Warning: Variable Val{:z}() is not defined.
└ @ ClimaCoupler.Diagnostics ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Diagnostics.jl:89
[ Info: Saving coupler diagnostics:
[ Info:     diag_test_dir/x..0000-02-01T00:00:00.hdf5
┌ Warning: Variable Val{:z}() is not defined.
└ @ ClimaCoupler.Diagnostics ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Diagnostics.jl:89
┌ Warning: Variable Val{:z}() is not defined.
└ @ ClimaCoupler.Diagnostics ~/work/ClimaCoupler.jl/ClimaCoupler.jl/src/Diagnostics.jl:89
[ Info: Saving coupler diagnostics:
[ Info:     diag_test_dir/x..0000-02-01T00:00:00.hdf5
Test Summary:     | Pass  Total  Time
Diagnostics tests |   26     26  3.5s
[ Info: No regridding required.
[ Info: No regridding required.
Test Summary:       | Pass  Total   Time
PostProcessor tests |    8      8  10.4s
[ Info: Saving checkpoint Unnamed model state to HDF5 on day 0 second 1
┌ Info: Setting 
│   Interfacer.name(sim) = "Unnamed"
└   " state to checkpoint: $(input_file), corresponding to day $(day) second $(sec)" = " state to checkpoint: test_checkpoint/checkpoint/checkpoint_Unnamed_1.hdf5, corresponding to day 0 second 1"
Test Summary:      | Pass  Total  Time
Checkpointer tests |    3      3  0.7s
Test Summary:                      | Pass  Total   Time
experiment test: CoupledSims tests |   14     14  11.8s
┌ Warning: Module ClimaCoreTempestRemap with build ID ffffffff-ffff-ffff-0000-00abec8f15ee is missing from the cache.
│ This may mean ClimaCoreTempestRemap [d934ef94-cdd4-4710-83d6-720549644b70] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1948
WARNING: Makie.Combined is deprecated, use Plot instead.
  likely near none:1
WARNING: importing deprecated binding Makie.Combined into CairoMakie.
, use Plot instead.
WARNING: Makie.ContinuousSurface is deprecated, use VertexGrid instead.
  likely near none:1
WARNING: importing deprecated binding Makie.ContinuousSurface into CairoMakie.
, use VertexGrid instead.
WARNING: Makie.DiscreteSurface is deprecated, use CellGrid instead.
  likely near none:1
WARNING: importing deprecated binding Makie.DiscreteSurface into CairoMakie.
, use CellGrid instead.
@juliasloan25 juliasloan25 mentioned this issue Oct 11, 2024
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@juliasloan25
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partially addressed in #1013, but there are still more warnings to remove

@juliasloan25
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juliasloan25 commented Oct 25, 2024 •
edited
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Note that the Plots.jl-related warnings (e.g. below) come from upstream plotting packages that are in the process of being fixed as of 10/25/24. For more information see the thread in JuliaIO/ImageMagick.jl#235. This should be fixed via patch releases, so we won't have to do anything to inherit the fixes.

Edit: it looks like this was just fixed today! :)

┌ Plots
│  WARNING: using deprecated binding Colors.RGB1 in PlotUtils.
│  , use XRGB instead.
│  WARNING: using deprecated binding PlotUtils.RGB1 in Plots.
│  , use ColorTypes.XRGB{T} where T<:Union{AbstractFloat, FixedPointNumbers.FixedPoint{T, f} where f where T<:Integer} instead.
│  WARNING: using deprecated binding Colors.RGB4 in PlotUtils.
│  , use RGBX instead.
│  WARNING: using deprecated binding PlotUtils.RGB4 in Plots.
│  , use ColorTypes.RGBX{T} where T<:Union{AbstractFloat, FixedPointNumbers.FixedPoint{T, f} where f where T<:Integer} instead.
└

@juliasloan25 juliasloan25 mentioned this issue Oct 25, 2024
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Fix more test warnings CliMA/ClimaCoupler.jl
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@Sbozzolo @juliasloan25