Installation Issue about baysor

[BoomStarcuc]

Hi, @VPetukhov

The version of Baysor 0.5.2 with Julia 1.7.3 works for me. Thank you for your help!!!

Best
YW

[VPetukhov]

@BoomStarcuc , Julia updated their Manifest language in version 1.7, so when I recompiled it under the version, the support for lower versions was dropped. Sorry for that, but you either need to install Julia 1.7 or use an older version of Baysor: Pkg.add(PackageSpec(url="https://github.com/hms-dbmi/Baysor.git", rev="0.5.1"))

[BoomStarcuc]

Hi, @VPetukhov

Thank you for your information!!!

After installing Julia 1.6.0 and then running the command '''Pkg.add(PackageSpec(url="https://github.com/hms-dbmi/Baysor.git", rev="0.5.1"))''', I got the errors as follows:

julia > Pkg.add(PackageSpec(url="https://github.com/hms-dbmi/Baysor.git", rev="0.5.1"))
Cloning git-repo https://github.com/hms-dbmi/Baysor.git
Updating git-repo https://github.com/hms-dbmi/Baysor.git
ERROR: Did not find rev 0.5.1 in repository

Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:55
[2] (::Pkg.Types.var"#44#45"{Pkg.Types.Context, Pkg.Types.PackageSpec, String})(repo::LibGit2.GitRepo)
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:634
[3] with(f::Pkg.Types.var"#44#45"{Pkg.Types.Context, Pkg.Types.PackageSpec, String}, obj::LibGit2.GitRepo)
@ LibGit2 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/LibGit2/src/types.jl:1150
[4] handle_repo_add!(ctx::Pkg.Types.Context, pkg::Pkg.Types.PackageSpec)
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:619
[5] handle_repos_add!(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:686
[6] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:177
[7] add
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:148 [inlined]
[8] add(pkgs::Vector{Pkg.Types.PackageSpec}; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:73
[9] add
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:72 [inlined]
[10] #add#20
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:69 [inlined]
[11] add(pkg::Pkg.Types.PackageSpec)
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:69
[12] top-level scope
@ REPL[4]:1

I also try other commands,like ''Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git", rev="0.5.1"))" and "Pkg.add([PackageSpec(name="UMAP", rev="0.5.1"), PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")])", which did not work. Could you give some advice?

Thank you very much again.

Best
YW

[BoomStarcuc]

Hi, @VPetukhov

I successfully run the command.

baysor run -i 50 --force-2d --num-cells-init 20 -s 14 -c /configs/iss.toml -o ./output_no_dapi ./data/pciSeq_3-3.csv

But when I want to visualize cell borders using -p, I got errors as follows:

[22:31:10] Info: Plot diagnostics
ERROR: LoadError: UndefRefError: access to undefined reference
Stacktrace:
[1] getproperty
@ ./Base.jl:42 [inlined]
[2] show
@ ~/.julia/packages/Makie/6TJFL/src/makielayout/blocks/axis.jl:1205 [inlined]
[3] show_delim_array(io::IOContext{IOBuffer}, itr::Tuple{NamedTuple{(:font,), Tuple{String}}, typeof(Makie.initialize_block!), Makie.Axis}, op::Char, delim::Char, cl::Char, delim_one::Bool, i1::Int64, n::Int64)
@ Base ./show.jl:1244
[4] show_delim_array
@ ./show.jl:1229 [inlined]
[5] show(io::IOContext{IOBuffer}, t::Tuple{NamedTuple{(:font,), Tuple{String}}, typeof(Makie.initialize_block!), Makie.Axis})
@ Base ./show.jl:1262
[6] _show_default(io::IOBuffer, x::Any)
@ Base ./show.jl:413
[7] show_default
@ ./show.jl:396 [inlined]
[8] show
@ ./show.jl:391 [inlined]
[9] print(io::IOBuffer, x::MethodError)
@ Base ./strings/io.jl:35
[10] print_to_string(::MethodError, ::Vararg{Any})
@ Base ./strings/io.jl:144
[11] string(::MethodError, ::String)
@ Base ./strings/io.jl:185
[12] macro expansion
@ ./logging.jl:360 [inlined]
[13] run_cli(args::Vector{String})
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/common.jl:170
[14] run_cli()
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/common.jl:137
[15] top-level scope
@ ~/anaconda3/envs/baysor/Baysor-0.5.2/bin/baysor:3
in expression starting at /home/jcl3689/anaconda3/envs/baysor/Baysor-0.5.2/bin/baysor:3

caused by: MethodError: no method matching initialize_block!(::Makie.Axis; font="Helvetica")
Closest candidates are:
initialize_block!(::Makie.Axis; palette) at ~/.julia/packages/Makie/6TJFL/src/makielayout/blocks/axis.jl:168 got unsupported keyword argument "font"
initialize_block!(::Makie.Colorbar) at ~/.julia/packages/Makie/6TJFL/src/makielayout/blocks/colorbar.jl:81 got unsupported keyword argument "font"
initialize_block!(::Makie.Axis3) at ~/.julia/packages/Makie/6TJFL/src/makielayout/blocks/axis3d.jl:3 got unsupported keyword argument "font"
...
Stacktrace:
[1] kwerr(::NamedTuple{(:font,), Tuple{String}}, ::Function, ::Makie.Axis)
@ Base ./error.jl:163
[2] block(::Type{Makie.Axis}, ::Makie.Figure; bbox::Nothing, kwargs::Base.Pairs{Symbol, Any, NTuple{10, Symbol}, NamedTuple{(:title, :xticksvisible, :yticksvisible, :xticklabelsize, :yticklabelsize, :xlabel, :ylabel, :xlabelpadding, :ylabelpadding, :font), Tuple{String, Bool, Bool, Int64, Int64, String, String, Int64, Int64, String}}})
@ Makie ~/.julia/packages/Makie/6TJFL/src/makielayout/blocks.jl:403
[3] ##993
@ ~/.julia/packages/Makie/6TJFL/src/makielayout/blocks.jl:279 [inlined]
[4] plot_num_of_cells_per_iterarion(tracer::Dict{Symbol, Any})
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/data_processing/plots.jl:155
[5] (::Baysor.var"#329#330"{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, DataFrames.DataFrame, Vector{Int64}, Dict{Symbol, Any}})(io::IOStream)
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/main.jl:162
[6] open(::Baysor.var"#329#330"{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, DataFrames.DataFrame, Vector{Int64}, Dict{Symbol, Any}}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Base ./io.jl:330
[7] open
@ ./io.jl:328 [inlined]
[8] plot_diagnostics_panel(df_res::DataFrames.DataFrame, assignment::Vector{Int64}, tracer::Dict{Symbol, Any}, args::Dict{String, Any}; clust_res::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing)
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/main.jl:142
[9] save_segmentation_results(bm_data::Baysor.BmmData{3}, gene_names::Vector{String}, args::Dict{String, Any}; mol_clusts::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing, prior_polygons::Vector{Matrix{Float64}})
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/main.jl:412
[10] run_cli_main(args::Vector{String})
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/main.jl:481
[11] run_cli(args::Vector{String})
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/common.jl:152
[12] run_cli()
@ Baysor ~/.julia/packages/Baysor/K7Vqu/src/cli/common.jl:137
[13] top-level scope
@ ~/anaconda3/envs/baysor/Baysor-0.5.2/bin/baysor:3

I also looked for some solutions for this error, but it did not work. Should I install old version of Baysor 0.5.1 to try it? If so, could you tell me the correct julia command for old version of baysor 0.5.1

@BoomStarcuc , Julia updated their Manifest language in version 1.7, so when I recompiled it under the version, the support for lower versions was dropped. Sorry for that, but you either need to install Julia 1.7 or use an older version of Baysor: Pkg.add(PackageSpec(url="https://github.com/hms-dbmi/Baysor.git", rev="0.5.1"))

Sorry for your inconvenience. I am new for julia, so I really appreciate if you could give me some help or advice?

Best
YW

[IMJoeyZhu]

Hi, @VPetukhov

The version of Baysor 0.5.2 with Julia 1.7.3 works for me. Thank you for your help!!!

Best YW

Hello! What system are you using? MacOS or Linux system? And which version is the system?

[VPetukhov]

Please, see the response in #59 . Should be resolved in v0.6.0.