Adding NetCDF_jll explicitly caused the GMT.jl version to be downgraded to v0.44.8

[melodyjulia]

This happened on macOS, while it works fine on Linux.
If specifying GMT.jl v1.28.1 for installation, the following prompt appeared:

  [5752ebe1] ↑ GMT v0.44.8 ⇒ v1.28.1
⌅ [7243133f] ↓ NetCDF_jll v401.900.300+0 ⇒ v400.902.211+1
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [5752ebe1] ↑ GMT v0.44.8 ⇒ v1.28.1
  [66db9d55] - SnoopPrecompile v1.0.3
⌃ [a7073274] ↓ GDAL_jll v302.1000.200+0 ⇒ v302.1000.100+0
  [b68b8c3f] + GMT_jll v6.5.3+1
  [61579ee1] + Ghostscript_jll v9.55.0+4
  [818ab7a1] - HDF4_jll v4.3.1+0
⌅ [0234f1f7] ↓ HDF5_jll v1.14.6+0 ⇒ v1.14.3+3
  [17f450c3] + LAPACK32_jll v3.12.0+1
  [8372b9c3] + LASzip_jll v3.4.3000+0
  [6a1430e4] + Leptonica_jll v1.85.0+0
⌅ [7243133f] ↓ NetCDF_jll v401.900.300+0 ⇒ v400.902.211+1
  [656ef2d0] + OpenBLAS32_jll v0.3.29+0
⌅ [fe0851c0] ↓ OpenMPI_jll v5.0.7+1 ⇒ v4.1.8+0
  [2f80f16e] + PCRE_jll v8.45.0+0
⌅ [784f63db] ↓ Qhull_jll v10008.0.1004+0 ⇒ v8.0.1004+0

[joa-quim]

I don't think this is due to any recent change in GMT.jl. Maybe on the adding of a HDF4 to GDAL_jll. Try doing

] add GMT@1.28.1

to se what Julia reports to be the versions conflicts.
That downgrade of NetCDF_jll seems the culprit to me. And there is also the option to use environments (which I personally hate but see their usefulness)

[melodyjulia]

What I shared previously was from the command add GMT@1.28.1.

If trying the command up, the following prompt appears:

    Updating registry at `~/.julia/registries/General.toml`
    Updating `~/.julia/environments/v1.11/Project.toml`
⌃ [5752ebe1] ↓ GMT v1.28.1 ⇒ v0.44.8
  [7243133f] ↑ NetCDF_jll v400.902.211+1 ⇒ v401.900.300+0
    Updating `~/.julia/environments/v1.11/Manifest.toml`
⌃ [5752ebe1] ↓ GMT v1.28.1 ⇒ v0.44.8
  [66db9d55] + SnoopPrecompile v1.0.3
  [a7073274] ↑ GDAL_jll v302.1000.100+0 ⇒ v302.1000.200+0
  [b68b8c3f] - GMT_jll v6.5.3+1
  [61579ee1] - Ghostscript_jll v9.55.0+4
  [818ab7a1] + HDF4_jll v4.3.1+0
  [0234f1f7] ↑ HDF5_jll v1.14.3+3 ⇒ v1.14.6+0
  [17f450c3] - LAPACK32_jll v3.12.0+1
  [8372b9c3] - LASzip_jll v3.4.3000+0
  [6a1430e4] - Leptonica_jll v1.85.0+0
  [7243133f] ↑ NetCDF_jll v400.902.211+1 ⇒ v401.900.300+0
  [656ef2d0] - OpenBLAS32_jll v0.3.29+0
  [fe0851c0] ↑ OpenMPI_jll v4.1.8+0 ⇒ v5.0.7+1
  [2f80f16e] - PCRE_jll v8.45.0+0
  [784f63db] ↑ Qhull_jll v8.0.1004+0 ⇒ v10008.0.1004+0

I'm curious about why HDF4 causes such significant degradation in GMT.jl.

[joa-quim]

I don't know if it's HDF4, I mentioned it because it's a recent addition to GDAL_jll and because, for example I'm not able to make it install in my WSL version.
Don't know much more what to tell you. All dependencies shown seem to be the newest available but still something is causing the GMT downgrade. Try to remove GMT ] rm GMT and add it back again.

[melodyjulia]

Removing and reinstalling GMT hasn't resolved the issue. Are there any other solutions I could try?

[melodyjulia]

It appears that NetCDF_jll, which was added previously, is causing the problem, regardless of whether it's on macOS or Linux systems. If NetCDF_jll is removed, running up will update GMT.jl to version 1.28.1. However, if I attempt to add NetCDF_jll and up again, GMT.jl will be downgraded back to version 0.44.8.

The NetCDF_jll is implicitly required by both NCDatasets.jl and NetCDF.jl, which are already installed. I don't understand why explicitly installing NetCDF_jll would trigger a downgrade of GMT.jl.

[joa-quim]

One normally do not install *_jll packages directly but let the dependency machinery decide what to install. If removing NetCDF_jll solves the problem (I must find out why but the dependency rules are very complex in Julia), use that solution (an appropriate NetCDF_jll will be installed for sure).

And there is always the virtual environments, like I mentioned above.
https://pkgdocs.julialang.org/v1/getting-started/#Getting-Started-with-Environments

[melodyjulia]

Thanks. NetCDF_jll was installed explicitly some time ago, and it hadn't caused any issues until recently.

[joa-quim]

Can we close this issue?

[melodyjulia]

Yes, please. However, installing NetCDF_jll still triggers the downgrading of GMT.jl.

[joa-quim]

Don«t know why. Maybe you have some package that forces to install an old NetCDF_jll, that forces the downgrade of GMT.jl
I don't get that in Linux

(@v1.10) pkg> st
Status `~/.julia/environments/v1.10/Project.toml`
  [5752ebe1] GMT v1.28.2
  [85f8d34a] NCDatasets v0.14.7
⌃ [c3e4b0f8] Pluto v0.20.5
⌃ [26020ff4] RemoteS v1.3.3
⌃ [295af30f] Revise v3.7.3
⌅ [7243133f] NetCDF_jll v400.902.211+1

[melodyjulia]

I found if pinning NetCDF_jll at version v400.902.211, everything is ok. But if updating NetCDF_jll to v401.900.300, the GMT.jl would be downgraded to v0.44.8.

[joa-quim]

I can reproduce that too. Possibly it's because the GMT_jll has this compat line

Dependency("NetCDF_jll", compat="400.902.210")

I'll try to update it when GDAL_jll uptates to GDAL 3.11. But I'm always very scared to change compats as I still can't make much sense on the Julia's compat system.

[joa-quim]

Is this fixed with the new GMT_jll?

[melodyjulia]

Yes, the master version fixed it. I can have NetCDF_jll (v400.902.211+1) coexisted with the newest GMT. Thank you!