new error related to HDF5
Closed this issue · 6 comments
Hi, i'm getting new error.
i wonder if this is going to be concerns.
i checked MIRT and plots are new version.
WARNING: could not import HDF5.Group into _hdf5_implementation
WARNING: could not import HDF5.Dataset into _hdf5_implementation
┌ Warning: Error requiring `HDF5` from `Plots`
│ exception =
│ LoadError: UndefVarError: Group not defined
│ Stacktrace:
│ [1] top-level scope
│ @ ~/.julia/packages/Plots/iYDwd/src/backends/hdf5.jl:162
│ [2] include(mod::Module, _path::String)
│ @ Base ./Base.jl:386
│ [3] include(x::String)
│ @ Plots ~/.julia/packages/Plots/iYDwd/src/Plots.jl:1
│ [4] top-level scope
│ @ ~/.julia/packages/Plots/iYDwd/src/init.jl:35
│ [5] eval
│ @ ./boot.jl:360 [inlined]
│ [6] eval
│ @ ~/.julia/packages/Plots/iYDwd/src/Plots.jl:1 [inlined]
│ [7] (::Plots.var"#270#303")()
│ @ Plots ~/.julia/packages/Requires/7Ncym/src/require.jl:99
│ [8] err(f::Any, listener::Module, modname::String)
│ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:47
│ [9] (::Plots.var"#269#302")()
│ @ Plots ~/.julia/packages/Requires/7Ncym/src/require.jl:98
│ [10] withpath(f::Any, path::String)
│ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:37
│ [11] (::Plots.var"#268#301")()
│ @ Plots ~/.julia/packages/Requires/7Ncym/src/require.jl:97
│ [12] listenpkg(f::Any, pkg::Base.PkgId)
│ @ Requires ~/.julia/packages/Requires/7Ncym/src/require.jl:20
│ [13] macro expansion
│ @ ~/.julia/packages/Requires/7Ncym/src/require.jl:95 [inlined]
│ [14] __init__()
│ @ Plots ~/.julia/packages/Plots/iYDwd/src/init.jl:33
│ [15] include
│ @ ./Base.jl:386 [inlined]
│ [16] _require(pkg::Base.PkgId)
│ @ Base ./loading.jl:1050
│ [17] require(uuidkey::Base.PkgId)
│ @ Base ./loading.jl:914
│ [18] require(into::Module, mod::Symbol)
│ @ Base ./loading.jl:901
│ [19] include(mod::Module, _path::String)
│ @ Base ./Base.jl:386
│ [20] include(x::String)
│ @ MIRT ~/.julia/packages/MIRT/O2fcB/src/MIRT.jl:7
│ [21] top-level scope
│ @ ~/.julia/packages/MIRT/O2fcB/src/plot/z-list.jl:3
│ [22] include(mod::Module, _path::String)
│ @ Base ./Base.jl:386
│ [23] include(x::String)
│ @ MIRT ~/.julia/packages/MIRT/O2fcB/src/MIRT.jl:7
│ [24] top-level scope
│ @ ~/.julia/packages/MIRT/O2fcB/src/z-all.jl:4
│ [25] include(mod::Module, _path::String)
│ @ Base ./Base.jl:386
│ [26] include(x::String)
│ @ MIRT ~/.julia/packages/MIRT/O2fcB/src/MIRT.jl:7
│ [27] top-level scope
│ @ ~/.julia/packages/MIRT/O2fcB/src/MIRT.jl:12
│ [28] include
│ @ ./Base.jl:386 [inlined]
│ [29] _require(pkg::Base.PkgId)
│ @ Base ./loading.jl:1050
│ [30] require(uuidkey::Base.PkgId)
│ @ Base ./loading.jl:914
│ [31] require(into::Module, mod::Symbol)
│ @ Base ./loading.jl:901
│ [32] eval
│ @ ./boot.jl:360 [inlined]
│ [33] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
│ @ Base ./loading.jl:1094
│ [34] include_string
│ @ ~/.julia/packages/Atom/5NgzM/src/utils.jl:286 [inlined]
│ [35] (::Atom.var"#202#207"{String, Int64, String, Module, Bool})()
│ @ Atom ~/.julia/packages/Atom/5NgzM/src/eval.jl:121
│ [36] withpath(f::Atom.var"#202#207"{String, Int64, String, Module, Bool}, path::String)
│ @ CodeTools ~/.julia/packages/CodeTools/VsjEq/src/utils.jl:30
│ [37] withpath(f::Function, path::String)
│ @ Atom ~/.julia/packages/Atom/5NgzM/src/eval.jl:9
│ [38] (::Atom.var"#201#206"{String, Int64, String, Module, Bool})()
│ @ Atom ~/.julia/packages/Atom/5NgzM/src/eval.jl:119
│ [39] with_logstate(f::Function, logstate::Any)
│ @ Base.CoreLogging ./logging.jl:491
│ [40] with_logger
│ @ ./logging.jl:603 [inlined]
│ [41] #200
│ @ ~/.julia/packages/Atom/5NgzM/src/eval.jl:118 [inlined]
│ [42] hideprompt(f::Atom.var"#200#205"{String, Int64, String, Module, Bool})
│ @ Atom ~/.julia/packages/Atom/5NgzM/src/repl.jl:127
│ [43] macro expansion
│ @ ~/.julia/packages/Atom/5NgzM/src/eval.jl:117 [inlined]
│ [44] macro expansion
│ @ ~/.julia/packages/Media/ItEPc/src/dynamic.jl:24 [inlined]
│ [45] eval(text::String, line::Int64, path::String, mod::String, errorinrepl::Bool)
│ @ Atom ~/.julia/packages/Atom/5NgzM/src/eval.jl:114
│ [46] invokelatest(::Any, ::Any, ::Vararg{Any, N} where N; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
│ @ Base ./essentials.jl:708
│ [47] invokelatest(::Any, ::Any, ::Vararg{Any, N} where N)
│ @ Base ./essentials.jl:706
│ [48] macro expansion
│ @ ~/.julia/packages/Atom/5NgzM/src/eval.jl:41 [inlined]
│ [49] (::Atom.var"#184#185")()
│ @ Atom ./task.jl:411
│ in expression starting at /home/kangpyo/.julia/packages/Plots/iYDwd/src/backends/hdf5.jl:37
This looks like the same error here: JuliaPlots/Plots.jl#3235
yes, i show that. it belongs to MIRTio [(https://github.com/JeffFessler/MIRTio.jl)]
and stated
"This code is a package dependency of MIRT.jl so most users will never clone this repo directly. Installing MIRT by following the instructions at https://github.com/JeffFessler/MIRT.jl will automatically include this code through the magic of Julia's package manager."
so as I believe it should be included.
but not sure what do I need do?
thanks
temporarily you could use the master branch of MIRT:
]add MIRT#master
I am working on several updates to underlying packages that will solve this problem - hopefully pretty soon.
it shows another error with master
(@v1.6) pkg> add MIRT#master
Updating git-repo https://github.com/JeffFessler/MIRT.jl.git
Resolving package versions...
ERROR: Unsatisfiable requirements detected for package MIRTjim [170b2178]:
MIRTjim [170b2178] log:
├─possible versions are: 0.1.0-0.5.0 or uninstalled
└─restricted to versions 0.6 by MIRT [7035ae7a] — no versions left
└─MIRT [7035ae7a] log:
├─possible versions are: 0.13.3 or uninstalled
└─MIRT [7035ae7a] is fixed to version 0.13.3
I'm looking forward to getting the updated version.
thank you!
Ok, v14.0 of MIRT is now released and you can see that it is registered:
https://github.com/JuliaRegistries/General/blob/master/M/MIRT/Versions.toml
Please see if Pkg update will get you the new version now.
I fear that it will not due too some serious issue with the Pkg servers:
JuliaRegistries/General#16777
You can see that MIRTjim v0.6 is properly registered here:
https://github.com/JuliaRegistries/General/blob/master/M/MIRTjim/Versions.toml
But somehow the pkg servers do not seem to be syncing properly right now.
A workaround that worked for me is to use the github version of the Registry instead of the other servers:
using Pkg
Pkg.Registry.rm("General")
ENV["JULIA_PKG_SERVER"] = ""
]upPlease close this issue if this works for you.
it works!
thank you much