There seems to be two sources of this issue, both related binaries / BinaryBuilder (see e.g. JuliaPackaging/Yggdrasil#4105)
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.
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
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
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
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:
but at least the package loads.
Versioninfo: