MentaLiST installation in conda package has LoadError

[sean-la]

After installing PathOGiST via conda install pathogist and running the co-installed MentaLiST program using the command mentalist -h, I get the following error:

ERROR: LoadError: ArgumentError: Package Lumberjack not found in current path:
- Run `import Pkg; Pkg.add("Lumberjack")` to install the Lumberjack package.

Stacktrace:
 [1] require(::Module, ::Symbol) at ./loading.jl:823
 [2] include at ./boot.jl:326 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1038
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] exec_options(::Base.JLOptions) at ./client.jl:267
 [6] _start() at ./client.jl:436
in expression starting at /home/laseanl/Software/miniconda3/envs/pathogist/bin/mentalist:2

[sean-la]

Lumberjack is a logging package for Julia.

[sean-la]

Trying to install Lumberjack manually in Julia yields:

julia> using Pkg

julia> Pkg.add("Lumberjack")
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package Lumberjack [ff7a09a4]:
 Lumberjack [ff7a09a4] log:
 ├─possible versions are: [0.0.1-0.0.8, 1.0.0-1.0.1, 2.0.0-2.0.1, 2.1.0-2.1.1] or uninstalled
 ├─restricted to versions * by an explicit requirement, leaving only versions [0.0.1-0.0.8, 1.0.0-1.0.1, 2.0.0-2.0.1, 2.1.0-2.1.1]
 └─restricted by julia compatibility requirements to versions: uninstalled — no versions left
Stacktrace:
 [1] #propagate_constraints!#61(::Bool, ::Function, ::Pkg.GraphType.Graph, ::Set{Int64}) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/GraphType.jl:1007
 [2] propagate_constraints! at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/GraphType.jl:948 [inlined]
 [3] #simplify_graph!#121(::Bool, ::Function, ::Pkg.GraphType.Graph, ::Set{Int64}) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/GraphType.jl:1462
 [4] simplify_graph! at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/GraphType.jl:1462 [inlined] (repeats 2 times)
 [5] resolve_versions!(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Nothing) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:371
 [6] resolve_versions! at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:315 [inlined]
 [7] #add_or_develop#63(::Array{Base.UUID,1}, ::Symbol, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:1172
 [8] #add_or_develop at ./none:0 [inlined]
 [9] #add_or_develop#17(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:59
 [10] #add_or_develop at ./none:0 [inlined]
 [11] #add_or_develop#16 at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:36 [inlined]
 [12] #add_or_develop at ./none:0 [inlined]
 [13] #add_or_develop#13 at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:34 [inlined]
 [14] #add_or_develop at ./none:0 [inlined]
 [15] #add_or_develop#12(::Base.Iterators.Pairs{Symbol,Symbol,Tuple{Symbol},NamedTuple{(:mode,),Tuple{Symbol}}}, ::Function, ::String) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:33
 [16] #add_or_develop at ./none:0 [inlined]
 [17] #add#22 at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:64 [inlined]
 [18] add(::String) at /home/conda/feedstock_root/build_artifacts/julia_1560178187757/work/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:64
 [19] top-level scope at none:0

[sean-la]

Making a fresh install of Julia version 1.1.1 using conda and installing Lumberjack using Pkg.add("Lumberjack") yields the same unsatisfiability error, meaning that Lumberjack is incompatible with version 1.1.1 of Julia.

[sean-la]

Current MentaLiST bioconda package uses Julia version 0.6.1. The solution to this is to set the PathOGiST installation of Julia to be version v0.6.1.

[matnguyen]

Current MentaLiST bioconda package uses Julia version 0.6.1. The solution to this is to set the PathOGiST installation of Julia to be version v0.6.1.

So PathOGiST currently installs v1.1.1 of Julia?

[sean-la]

Yep!

[sean-la]

@matnguyen I've changed the julia version of PathOGiST to be 0.6.1 in the meta.yaml file. The conda package builds successfully. Would you be able to push the latest PathOGiST build to Bioconda?