installation problem ubuntu 22.04

[jkwashbourne-oss]

in order to get ]add GMT to work I had to do the following

sudo ln -s /lib/x86_64-linux-gnu/libgmt.so.6.3.0 /lib/x86_64-linux-gnu/libgmt.so

I dont know if this was a problem on my end or an expectation from GMT.

$ ls -lsa /lib/x86_64-linux-gnu/libgmt*
   0 lrwxrwxrwx 1 root root      37 Jun 16 17:39 /lib/x86_64-linux-gnu/libgmt.so -> /lib/x86_64-linux-gnu/libgmt.so.6.3.0
   0 lrwxrwxrwx 1 root root      15 Dec  9  2021 /lib/x86_64-linux-gnu/libgmt.so.6 -> libgmt.so.6.3.0
4792 -rw-r--r-- 1 root root 4903336 Dec  9  2021 /lib/x86_64-linux-gnu/libgmt.so.6.3.0

[joa-quim]

Hmm, that does not smell good. GMT.jl needs GMT 6.5 to work but in fact it installs its own version via the Pkg machinery. What do you get when run this on REPL?
GMTver

[joa-quim]

Ping.

[jkwashbourne-oss]

I will pull a fresh vm and try again. I am doing the installation from the repl, ]add GMT

[jkwashbourne-oss]

OK this time I see a problem with the install script. below is the log of my actions, but the key problem is below, I think deps.jl should be build.jl?

ERROR: LoadError: SystemError: opening file "/home/cvx/.julia/packages/GMT/1kBBX/deps/deps.jl": No such file or directory

(@v1.11) pkg> add GMT
    Updating registry at `~/.julia/registries/ChevronETC`
    Updating git-repo `https://chevron@dev.azure.com/chevron/ETC-ESD-PkgRegistry.jl/_git/PkgRegistry.jl`
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
   Installed Crayons ──────────── v4.1.1
   Installed StringManipulation ─ v0.4.1
   Installed SnoopPrecompile ──── v1.0.3
   Installed PrettyTables ─────── v2.4.0
   Installed GMT ──────────────── v0.44.8
    Updating `~/.julia/environments/v1.11/Project.toml`
⌃ [5752ebe1] + GMT v0.44.8
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [a8cc5b0e] + Crayons v4.1.1
⌃ [5752ebe1] + GMT v0.44.8
  [08abe8d2] + PrettyTables v2.4.0
  [66db9d55] + SnoopPrecompile v1.0.3
  [892a3eda] + StringManipulation v0.4.1
        Info Packages marked with ⌃ have new versions available and may be upgradable.
    Building GMT → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/5968385e86d9c119db96d05e41df420c245f73da/build.log`
Precompiling project...
  ✗ GMT
  4 dependencies successfully precompiled in 72 seconds. 406 already precompiled.
  1 dependency errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

(@v1.11) pkg> precompile
Precompiling project...
  ✗ GMT
  0 dependencies successfully precompiled in 2 seconds. 410 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

GMT 

Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/home/cvx/.julia/compiled/v1.11/GMT/jl_C8VOlX".
ERROR: LoadError: SystemError: opening file "/home/cvx/.julia/packages/GMT/1kBBX/deps/deps.jl": No such file or directory
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base ./error.jl:176
  [2] systemerror
    @ ./error.jl:175 [inlined]
  [3] open(fname::String; lock::Bool, read::Bool, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
    @ Base ./iostream.jl:295
  [4] open
    @ ./iostream.jl:277 [inlined]
  [5] open(fname::String, mode::String; lock::Bool)
    @ Base ./iostream.jl:358
  [6] open(fname::String, mode::String)
    @ Base ./iostream.jl:357
  [7] open(::typeof(Base._crc32c), ::String, ::Vararg{String}; kwargs::@Kwargs{})
    @ Base ./io.jl:408
  [8] open
    @ ./io.jl:407 [inlined]
  [9] macro expansion
    @ ./loading.jl:2101 [inlined]
 [10] macro expansion
    @ ./lock.jl:273 [inlined]
 [11] _include_dependency(mod::Module, _path::String; track_content::Bool, path_may_be_dir::Bool)
    @ Base ./loading.jl:2099
 [12] _include_dependency
    @ ./loading.jl:2084 [inlined]
 [13] _include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./loading.jl:2695
 [14] include(mod::Module, _path::String)
    @ Base ./Base.jl:557
 [15] include(x::String)
    @ GMT ~/.julia/packages/GMT/1kBBX/src/GMT.jl:1
 [16] top-level scope
    @ ~/.julia/packages/GMT/1kBBX/src/GMT.jl:34
 [17] include
    @ ./Base.jl:557 [inlined]
 [18] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2790
 [19] top-level scope
    @ stdin:5
in expression starting at /home/cvx/.julia/packages/GMT/1kBBX/src/GMT.jl:1
in expression starting at stdin:

[jkwashbourne-oss]

this may be a problem specific to my company firewall, as I see SSL errors when running julia /home/cvx/.julia/packages/GMT/1kBBX/deps/build.jl

Collecting package metadata (repodata.json): - Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1017)'))': /pkgs/main/linux-64/repodata.json.zst

[jkwashbourne-oss]

For what its worth, I proceeded by doing

sudo apt-get install -y gmt gmt-common

and then

julia  /home/cvx/.julia/packages/GMT/1kBBX/deps/build.jl

which brings us to the library link error above. apologies for the convoluted path here.

julia  /home/cvx/.julia/packages/GMT/1kBBX/deps/build.jl 
ldd: /usr/lib/x86_64-linux-gnu/libgmt.so: No such file or directory

sudo ln -s /usr/lib/x86_64-linux-gnu/libgmt.so.6.3.0 /usr/lib/x86_64-linux-gnu/libgmt.so
julia  /home/cvx/.julia/packages/GMT/1kBBX/deps/build.jl     [runs successfully with no output]

[jkwashbourne-oss]

so ... final comment ... the issue that is maybe actionable here is the install looking for deps.jl not build.jl

[joa-quim]

Installed GMT ──────────────── v0.44.8

This is not good. I have learned of an issue with the netcdf_jll library that when old would make this regression in GMT.jl version.
But this has been fixed with latest GMT_jll. And BTW, current GMT.jl version is 1.30

sudo apt-get install -y gmt gmt-common

You should not do that either (for using GMT in Julia). If you have GMT.jl installed (which I think you don't) and doing ? GMT shows this.

  The GMT.jl default is to use the GMT_jll artifact. However, this can be changed to use a system wide GMT installation. All
  info is stored in the deps/deps.jl file that is created by compile from the deps/build.jl. To swap to a system wide GMT
  installation, do (in REPL):

    •  ENV["SYSTEMWIDE_GMT"] = 1;

    •  import Pkg; Pkg.build("GMT")

    •  restart Julia

  Note the above will work up until some other reason triggers a Julia recompile, where the JLL artifacts will be used again.
  To make the ENV["SYSTEMWIDEGMT"] = 1 solution permanent, declare a "SYSTEMWIDEGMT" environment variable permanently in your
  .bashrc (or whatever).

but this is meant for one builds GMT ourselves and have reasons to use our own GMT version.

To try to solve your case. Try removing GMT.jl (] rm GMT) and add it again.