GMT.jl error after upgrading Julia

Q&A GMT.jl Q&A
1

I recently upgraded to Version 1.7.2. Is there anything I need to do to make my GMT.jl to continue to work?

Below is the error I’m having right now. Many thanks.

error: /Library/Developer/CommandLineTools/usr/bin/otool-classic: can't open file: @rpath/libgdal.29.dylib (No such file or directory)
ERROR: LoadError: failed processes:
  Process(`otool -L @rpath/libgdal.29.dylib`, ProcessExited(1)) [1]
  Process(`grep libproj`, ProcessExited(1)) [1]

Stacktrace:
  [1] pipeline_error(procs::Base.ProcessChain)
    @ Base ./process.jl:544
  [2] (::Base.var"#697#698"{Base.ProcessChain})()
    @ Base ./process.jl:320
  [3] iterate(itr::Base.EachLine{Base.PipeEndpoint}, state::Nothing) (repeats 2 times)
    @ Base ./io.jl:1019
  [4] _collect(cont::UnitRange{Int64}, itr::Base.EachLine{Base.PipeEndpoint}, #unused#::Base.HasEltype, isz::Base.SizeUnknown)
    @ Base ./array.jl:660
  [5] collect
    @ ./array.jl:649 [inlined]
  [6] #readlines#378
    @ ./io.jl:553 [inlined]
  [7] readlines(s::Base.OrCmds)
    @ Base ./io.jl:553
  [8] top-level scope
    @ ~/.julia/packages/GMT/dEogU/src/GMT.jl:62
  [9] include
    @ ./Base.jl:418 [inlined]
 [10] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1318
 [11] top-level scope
    @ none:1
 [12] eval
    @ ./boot.jl:373 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [14] top-level scope
    @ none:1
in expression starting at /Users/leon.julia/packages/GMT/dEogU/src/GMT.jl:1
ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to /Users/leon/.julia/compiled/v1.7/GMT/jl_iuUWKA.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1466
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1410
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1120
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1013
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:997
2

??? version 1.7.2 of what?

It seems a entirely a GDAL installation issue. I guess running GMT from the shell won’t work either, right?

1 Like
3

Many thanks for the reply.

Version 1.7.2 of Julia.

That is correct, I’m getting a bunch of errors by either typing using GMT within Julia, or using julia xxxx.jl

Is it normal to have GMT.jl corrupted by upgrading Julia? What is the fix?

4

Updating Julia has nothing to do with GMT.jl functioning. But you need to re-install the Julia packages after updates.
My question was. Does GMT run from the shell?

5

Sorry but how do I run GMT from the shell? I mainly use it through Julia.

When I type GMT in the shell, I got the below successfully:

	GMT - The Generic Mapping Tools, Version 6.2.0 [64-bit] [16 cores]
	(c) 1991-2021 The GMT Team (https://www.generic-mapping-tools.org/team.html).

	Supported in part by the US National Science Foundation (http://www.nsf.gov/)
	and volunteers from around the world.

	GMT is distributed under the GNU LGPL License (http://www.gnu.org/licenses/lgpl.html).
	Dependencies: netCDF, GDAL, PCRE, FFTW, LAPACK, ZLIB, Ghostscript, GraphicsMagick, FFmpeg.

usage: gmt [options]
       gmt <module name> [<module-options>]

options:
  --help              List descriptions of available GMT modules.
  --new-script[=L]    Write GMT modern mode script template to stdout.
                      Optionally specify bash|csh|batch [Default is current shell].
  --new-glue=name     Write C code for external supplements to glue them to GMT.
  --show-bindir       Show directory with GMT executables.
  --show-citation     Show the most recent citation for GMT.
  --show-classic      Show all classic module names.
  --show-classic-core Show all classic module names (core only).
  --show-cores        Show number of available cores.
  --show-datadir      Show directory/ies with user data.
  --show-dataserver   Show URL of the remote GMT data server.
  --show-doi          Show the DOI for the current release.
  --show-library      Show path of the shared GMT library.
  --show-modules      Show all modern module names.
  --show-modules-core Show all modern module names (core only).
  --show-plugindir    Show directory for plug-ins.
  --show-sharedir     Show directory for shared GMT resources.
  --show-userdir      Show full path of user's ~/.gmt dir
  --version           Print GMT version number.

if <module-options> is '=' we call exit (0) if module exist and non-zero otherwise.
6

So that means GMT is working fine. Confess I’m lost with your GMT.jl problem. As I said when updating one must reinstall all the packages.
Try to remove GMT.jl and reinstall it again. I never had that problem.

1 Like