PlotlyJS error

elm9742 · November 1, 2024, 12:15am

I’m trying to do analysis using a package called scLENS.
I followed the guide code as shown on the scLENS GitHub, and when I run Pkg.instantiate(), I get the following error related to the PlotlyJS package.

  ✗ PlotlyJS
  ✗ PlotlyJS → DataFramesExt
  ✗ PlotlyJS → CSVExt
  ✗ scLENS
  0 dependencies successfully precompiled in 71 seconds. 232 already precompiled.
  4 dependencies errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

I’m not familiar with Julia, so I don’t know what this error is or how to fix it.
How can I solve it?

Thank you for help!

jd-foster · November 1, 2024, 1:24am

Welcome to the forum. Can you type err into the REPL after the error occurs and post the result here?

elm9742 · November 1, 2024, 4:44am

When I run err in REPL, the error message that occurs is too long to post in its entirety. First, the error message that appears on the top line is as follows.

PkgPrecompileError: The following 4 direct dependencies failed to precompile:

DataFramesExt

Failed to precompile DataFramesExt [69fdaafc-7253-5aa8-966e-acd4d6b210e1] to "C:\\Users\\ssu97\\.julia\\compiled\\v1.11\\DataFramesExt\\jl_ADF4.tmp".
ERROR: LoadError: InitError: AssertionError: isfile(f)
Stacktrace:
  [1] resource
    @ C:\Users\ssu97\.julia\packages\Blink\tnO3a\src\content\server.jl:5 [inlined]
  [2] resource(f::String)
    @ Blink C:\Users\ssu97\.julia\packages\Blink\tnO3a\src\content\server.jl:5
  [3] macro expansion
    @ C:\Users\ssu97\.julia\packages\Blink\tnO3a\src\AtomShell\webio.jl:34 [inlined]
  [4] (::Blink.AtomShell.var"#22#23")()
    @ Blink.AtomShell C:\Users\ssu97\.julia\packages\Lazy\9Xnd3\src\macros.jl:346
  [5] __init__()
    @ Blink.AtomShell C:\Users\ssu97\.julia\packages\Lazy\9Xnd3\src\macros.jl:341
  [6] run_module_init(mod::Module, i::Int64)
    @ Base .\loading.jl:1336
  [7] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base .\loading.jl:1324
  [8] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base .\loading.jl:1213
  [9] _include_from_serialized (repeats 2 times)
    @ .\loading.jl:1169 [inlined]
 [10] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base .\loading.jl:1985
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:2450
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2315
 [13] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2302
 [16] macro expansion
    @ .\loading.jl:2241 [inlined]
 [17] macro expansion
    @ .\lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2198
 [19] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2191
 [22] include
    @ .\Base.jl:557 [inlined]
 [23] 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::String)
    @ Base .\loading.jl:2790
 [24] top-level scope
    @ stdin:5
during initialization of module AtomShell
in expression starting at C:\Users\ssu97\.julia\packages\PlotlyJS\jwzG2\src\PlotlyJS.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile PlotlyJS [f0f68f2c-4968-5e81-91da-67840de0976a] to "C:\\Users\\ssu97\\.julia\\compiled\\v1.11\\PlotlyJS\\jl_AEDB.tmp".   
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base .\loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base .\loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile C:\Users\ssu97\.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:95
  [5] #mkpidlock#6
    @ C:\Users\ssu97\.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile C:\Users\ssu97\.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:116
  [7] #invokelatest#2
    @ .\essentials.jl:1057 [inlined]
  [8] invokelatest
    @ .\essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base .\loading.jl:3609
 [10] maybe_cachefile_lock
    @ .\loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2315
 [13] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2302
 [16] macro expansion
    @ .\loading.jl:2241 [inlined]
 [17] macro expansion
    @ .\lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2198
 [19] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2191
 [22] include
    @ .\Base.jl:557 [inlined]
 [23] 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:2790
 [24] top-level scope
    @ stdin:5
in expression starting at C:\Users\ssu97\.julia\packages\PlotlyJS\jwzG2\ext\DataFramesExt.jl:1
in expression starting at stdin:5
CSVExt

Failed to precompile CSVExt [6b5fe089-44ad-5ece-89e8-532c39ae1766] to "C:\\Users\\ssu97\\.julia\\compiled\\v1.11\\CSVExt\\jl_AE06.tmp".
ERROR: LoadError: InitError: AssertionError: isfile(f)
Stacktrace:
  [1] resource
    @ C:\Users\ssu97\.julia\packages\Blink\tnO3a\src\content\server.jl:5 [inlined]
  [2] resource(f::String)
    @ Blink C:\Users\ssu97\.julia\packages\Blink\tnO3a\src\content\server.jl:5
  [3] macro expansion
    @ C:\Users\ssu97\.julia\packages\Blink\tnO3a\src\AtomShell\webio.jl:34 [inlined]
  [4] (::Blink.AtomShell.var"#22#23")()
    @ Blink.AtomShell C:\Users\ssu97\.julia\packages\Lazy\9Xnd3\src\macros.jl:346
  [5] __init__()
    @ Blink.AtomShell C:\Users\ssu97\.julia\packages\Lazy\9Xnd3\src\macros.jl:341
  [6] run_module_init(mod::Module, i::Int64)
    @ Base .\loading.jl:1336
  [7] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base .\loading.jl:1324
  [8] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base .\loading.jl:1213
  [9] _include_from_serialized (repeats 2 times)
    @ .\loading.jl:1169 [inlined]
 [10] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base .\loading.jl:1985
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:2450
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2315
 [13] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2302
 [16] macro expansion
    @ .\loading.jl:2241 [inlined]
 [17] macro expansion
    @ .\lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2198
 [19] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2191
 [22] include
    @ .\Base.jl:557 [inlined]
 [23] 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::String)
    @ Base .\loading.jl:2790
 [24] top-level scope
    @ stdin:5
during initialization of module AtomShell
in expression starting at C:\Users\ssu97\.julia\packages\PlotlyJS\jwzG2\src\PlotlyJS.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile PlotlyJS [f0f68f2c-4968-5e81-91da-67840de0976a] to "C:\\Users\\ssu97\\.julia\\compiled\\v1.11\\PlotlyJS\\jl_BCA6.tmp".   
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base .\loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base .\loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile C:\Users\ssu97\.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:95
  [5] #mkpidlock#6
    @ C:\Users\ssu97\.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile C:\Users\ssu97\.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:116
  [7] #invokelatest#2
    @ .\essentials.jl:1057 [inlined]
  [8] invokelatest
    @ .\essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base .\loading.jl:3609
 [10] maybe_cachefile_lock
    @ .\loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2315
 [13] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2302
 [16] macro expansion
    @ .\loading.jl:2241 [inlined]
 [17] macro expansion
    @ .\lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2198
 [19] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2191
 [22] include
    @ .\Base.jl:557 [inlined]
 [23] 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:2790
 [24] top-level scope
    @ stdin:5
in expression starting at C:\Users\ssu97\.julia\packages\PlotlyJS\jwzG2\ext\CSVExt.jl:1
in expression starting at stdin:5

elm9742 · November 4, 2024, 5:42am

Please check the comment I posted following this post.

jd-foster · November 9, 2024, 3:20am

This seems to be addressed in the most recent update to the package: see PlotlyJS error · Issue #2 · Mathbiomed/scLENS · GitHub