ERROR: LoadError: UndefVarError: @main not defined in Baysor

[bednarsky]

Hi, and thanks for the important package! I am trying to install baysor on my HPC for running sopa, where I have to install baysor separately (just adding this info for the case the above commands mess something up). I follow your instructions, slightly adapting them so I can run the installation from a script without prompts.

source ~/miniconda_link/etc/profile.d/conda.sh

cd ~/projects/project_name/sopa
mamba create --name sopa python=3.10
conda activate sopa
pip install -e ".[snakemake,baysor,tangram]" 

# need to separately install baysor (in addition to dependencies installed above)
# install julia (-s -- -y is to be non-interactive)
curl -fsSL https://install.julialang.org | sh -s -- -y

# reload path env variable so that it finds julia
source ~/.bashrc

# this will be created at ~/.julia/bin/baysor, need to make symlink if you don't like that location
julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.build()'

I get this error:

Updating git-repo `https://github.com/kharchenkolab/Baysor.git`
Updating registry at `~/.julia/registries/General.toml`

Resolving package versions...
No Changes to /path/to/user/.julia/environments/v1.11/Project.toml
No Changes to /path/to/user/.julia/environments/v1.11/Manifest.toml
Precompiling project...
✗ Baysor
302 dependencies successfully precompiled in 175 seconds. 40 already precompiled.

The following 1 direct dependency failed to precompile:

Baysor

Failed to precompile Baysor [cc9f9468-1fbe-11e9-0acf-e9460511877c] to "~/.julia/compiled/v1.11/Baysor/jl_1wAons".
WARNING: both Comonicon and Base export "@main"; uses of it in module Baysor must be qualified
ERROR: LoadError: UndefVarError: @main not defined in Baysor
Suggestion: check for spelling errors or missing imports.
Hint: a global variable of this name also exists in Base.
Stacktrace:
[1] top-level scope
@ :0
[2] include
@ ./Base.jl:557 [inlined]
[3] 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:2806
[4] top-level scope
@ stdin:4
in expression starting at ~/.julia/packages/Baysor/0jqIq/src/Baysor.jl:24
in expression starting at ~/.julia/packages/Baysor/0jqIq/src/Baysor.jl:1
Building HDF5 ──→ ~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log
Building Baysor → ~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/e641fb17189f28e018ca48efcd1b9b9e19c137e0/build.log
ERROR: Error building Baysor:
Precompiling Baysor...
Info Given Baysor was explicitly requested, output will be shown live
[ Info: disable lazy package loading: environment variable LazyModules_lazyload=false is detected
WARNING: both Comonicon and Base export "@main"; uses of it in module Baysor must be qualified
ERROR: LoadError: UndefVarError: @main not defined in Baysor
Suggestion: check for spelling errors or missing imports.
Hint: a global variable of this name also exists in Base.
Stacktrace:
[1] top-level scope
@ :0
[2] include
@ ./Base.jl:557 [inlined]
[3] 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:2806
[4] top-level scope
@ stdin:4
in expression starting at ~/.julia/packages/Baysor/0jqIq/src/Baysor.jl:24
in expression starting at ~/.julia/packages/Baysor/0jqIq/src/Baysor.jl:1
in expression starting at stdin:4
✗ Baysor
0 dependencies successfully precompiled in 20 seconds. 342 already precompiled.

ERROR: LoadError: The following 1 direct dependency failed to precompile:

Baysor

Failed to precompile Baysor [cc9f9468-1fbe-11e9-0acf-e9460511877c] to "~/.julia/compiled/v1.11/Baysor/jl_yNDAss".
[ Info: disable lazy package loading: environment variable LazyModules_lazyload=false is detected
WARNING: both Comonicon and Base export "@main"; uses of it in module Baysor must be qualified
ERROR: LoadError: UndefVarError: @main not defined in Baysor
Suggestion: check for spelling errors or missing imports.
Hint: a global variable of this name also exists in Base.
Stacktrace:
[1] top-level scope
@ :0
[2] include
@ ./Base.jl:557 [inlined]
[3] 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:2806
[4] top-level scope
@ stdin:4
in expression starting at ~/.julia/packages/Baysor/0jqIq/src/Baysor.jl:24
in expression starting at ~/.julia/packages/Baysor/0jqIq/src/Baysor.jl:1
in expression starting at stdin:
in expression starting at ~/.julia/packages/Baysor/0jqIq/deps/build.jl:3
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68
[2] (::Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String})()
@ Pkg.Operations /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1177
[3] withenv(::Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}})
@ Base ./env.jl:265
[4] (::Pkg.Operations.var"#118#123"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec})()
@ Pkg.Operations /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1911
[5] with_temp_env(fn::Pkg.Operations.var"#118#123"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec}, temp_env::String)
@ Pkg.Operations /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1769
[6] (::Pkg.Operations.var"#116#121"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, String})(tmp::String)
@ Pkg.Operations /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1878
[7] mktempdir(fn::Pkg.Operations.var"#116#121"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, String}, parent::String; prefix::String)
@ Base.Filesystem ./file.jl:819
[8] mktempdir(fn::Function, parent::String)
@ Base.Filesystem ./file.jl:815
[9] mktempdir
@ ./file.jl:815 [inlined]
[10] #sandbox#115
@ /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1825 [inlined]
[11] build_versions(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}; verbose::Bool)
@ Pkg.Operations /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1158
[12] build_versions
@ /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1076 [inlined]
[13] build(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}, verbose::Bool)
@ Pkg.Operations /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1016
[14] build(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; verbose::Bool, kwargs::@kwargs{io::IOContext{IO}})
@ Pkg.API /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:1104
[15] build(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@kwargs{})
@ Pkg.API /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
[16] build(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:148
[17] build(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::@kwargs{})
@ Pkg.API /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:174
[18] build()
@ Pkg.API /path/to/user/.julia/juliaup/julia-1.11.0+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:165
[19] top-level scope
@ none:1

Would be really grateful for help!