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SeisIO v1.2.1 fails to compile on M1 Mac #93

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SeisIO v1.2.1 fails to compile on M1 Mac#93
#94
@haakon-e

Description

@haakon-e
haakon-e
opened on Oct 24, 2022

There seems to be two sources of this issue, both related binaries / BinaryBuilder (see e.g. JuliaPackaging/Yggdrasil#4105)

LightXML

This package is currently pinned to 0.8.1. Trying to precompile with that version leads to the following error:

LightXML error message 
(SeisIO) pkg> precompile
Precompiling project...
  ✗ BinaryProvider
  ✗ HDF5
  ✗ LightXML
  ✗ SeisIO
  0 dependencies successfully precompiled in 3 seconds. 47 already precompiled.

ERROR: The following 3 direct dependencies failed to precompile:

HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f]

Failed to precompile HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f] to /Users/username/.julia/compiled/v1.8/HDF5/jl_D5wiSh.
ERROR: LoadError: UndefVarError: libhdf5 not defined
Stacktrace:
 [1] h5_get_libversion()
   @ HDF5 ~/.julia/packages/HDF5/YX0jU/src/HDF5.jl:39
 [2] top-level scope
   @ ~/.julia/packages/HDF5/YX0jU/src/HDF5.jl:44
 [3] include
   @ ./Base.jl:419 [inlined]
 [4] 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::Nothing)
   @ Base ./loading.jl:1554
 [5] top-level scope
   @ stdin:1
in expression starting at /Users/username/.julia/packages/HDF5/YX0jU/src/HDF5.jl:1
in expression starting at stdin:1

SeisIO [b372bb87-02dd-52bb-bcf6-c30dd83fd342]

Failed to precompile SeisIO [b372bb87-02dd-52bb-bcf6-c30dd83fd342] to /Users/username/.julia/compiled/v1.8/SeisIO/jl_VPFNXy.
ERROR: LoadError: LightXML is not properly installed. Run `Pkg.build("LightXML")` and restart Julia.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] top-level scope
   @ ~/.julia/packages/LightXML/W8FVT/src/LightXML.jl:6
 [3] include
   @ ./Base.jl:419 [inlined]
 [4] 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:1554
 [5] top-level scope
   @ stdin:1
in expression starting at /Users/username/.julia/packages/LightXML/W8FVT/src/LightXML.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile LightXML [9c8b4983-aa76-5018-a973-4c85ecc9e179] to /Users/username/.julia/compiled/v1.8/LightXML/jl_EjhqTM.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [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::Nothing)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /Users/username/Documents/test/SeisIO.jl/src/SeisIO.jl:2
in expression starting at stdin:1


LightXML [9c8b4983-aa76-5018-a973-4c85ecc9e179]

Failed to precompile LightXML [9c8b4983-aa76-5018-a973-4c85ecc9e179] to /Users/username/.julia/compiled/v1.8/LightXML/jl_w9BwdH.
ERROR: LoadError: LightXML is not properly installed. Run `Pkg.build("LightXML")` and restart Julia.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] top-level scope
   @ ~/.julia/packages/LightXML/W8FVT/src/LightXML.jl:6
 [3] include
   @ ./Base.jl:419 [inlined]
 [4] 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::Nothing)
   @ Base ./loading.jl:1554
 [5] top-level scope
   @ stdin:1
in expression starting at /Users/username/.julia/packages/LightXML/W8FVT/src/LightXML.jl:2
in expression starting at stdin:1

Updating to 0.9.0 appears to resolve the issue.

HDF5

This package is currently pinned to 0.12.3 or 0.13. Trying to precompile with that version leads to the following error:

HDF5 error message 
(SeisIO) pkg> precompile
Precompiling project...
  ✗ HDF5
  ✗ SeisIO
  0 dependencies successfully precompiled in 6 seconds. 50 already precompiled.

ERROR: The following 2 direct dependencies failed to precompile:

HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f]

Failed to precompile HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f] to /Users/username/.julia/compiled/v1.8/HDF5/jl_chOIJJ.
ERROR: LoadError: UndefVarError: libhdf5 not defined
Stacktrace:
 [1] h5_get_libversion()
   @ HDF5 ~/.julia/packages/HDF5/YX0jU/src/HDF5.jl:39
 [2] top-level scope
   @ ~/.julia/packages/HDF5/YX0jU/src/HDF5.jl:44
 [3] include
   @ ./Base.jl:419 [inlined]
 [4] 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::Nothing)
   @ Base ./loading.jl:1554
 [5] top-level scope
   @ stdin:1
in expression starting at /Users/username/.julia/packages/HDF5/YX0jU/src/HDF5.jl:1
in expression starting at stdin:1

SeisIO [b372bb87-02dd-52bb-bcf6-c30dd83fd342]

Failed to precompile SeisIO [b372bb87-02dd-52bb-bcf6-c30dd83fd342] to /Users/username/.julia/compiled/v1.8/SeisIO/jl_xDakbk.
WARNING: method definition for GenResp at /Users/username/Documents/test/SeisIO.jl/src/Types/InstResp.jl:69 declares type variable T but does not use it.
ERROR: LoadError: UndefVarError: libhdf5 not defined
Stacktrace:
 [1] h5_get_libversion()
   @ HDF5 ~/.julia/packages/HDF5/YX0jU/src/HDF5.jl:39
 [2] top-level scope
   @ ~/.julia/packages/HDF5/YX0jU/src/HDF5.jl:44
 [3] include
   @ ./Base.jl:419 [inlined]
 [4] 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:1554
 [5] top-level scope
   @ stdin:1
in expression starting at /Users/username/.julia/packages/HDF5/YX0jU/src/HDF5.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f] to /Users/username/.julia/compiled/v1.8/HDF5/jl_mU2oQ3.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] include(x::String)
    @ SeisIO ~/Documents/test/SeisIO.jl/src/SeisIO.jl:2
 [11] top-level scope
    @ ~/Documents/test/SeisIO.jl/src/SeisIO.jl:141
 [12] include
    @ ./Base.jl:419 [inlined]
 [13] 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::Nothing)
    @ Base ./loading.jl:1554
 [14] top-level scope
    @ stdin:1
in expression starting at /Users/username/Documents/test/SeisIO.jl/src/Submodules/SeisHDF.jl:1
in expression starting at /Users/username/Documents/test/SeisIO.jl/src/SeisIO.jl:2
in expression starting at stdin:1

Updating to at least 0.14.2 appears to resolve the issue.

Comment:

I was not able to test SeisIO after bumping the package versions due to the following error:

ERROR: LoadError: download failed. Is a command-line SVN client installed?

    (type "run(`svn --version`)"; if an error occurs, SVN isn't installed.)

    Subversion for Ubuntu: sudo apt install subversion
    Subversion for OS X: pkg_add subversion
    SlikSVN Windows client: https://sliksvn.com/download/

but at least the package loads.

Versioninfo:

julia> versioninfo()
Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.3.0)
  CPU: 8 × Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
  Threads: 1 on 4 virtual cores

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