Can't read old JLD2 file


#1

i did an ] update and now i can’t read a .jld2 file made yesterday. a diff on the current and previous Manifest.toml files shows that only the DiffEqDiffTools, LsqFit, NLSolversBase, NaturalSort, Rotations, and WeakRefStrings packages have changed. activating a new empty test environment and installing JLD2 shows that it depends on none of these packages. can anyone explain how JLD2 is so fragile?


#2

What error message are you getting?


#3
**ERROR:** BoundsError: attempt to access 8249-element Array{Int64,1} at index [8250]

Stacktrace:

 [1] **getindex** at **./array.jl:731** [inlined]

 [2] **getindex** at **./multidimensional.jl:412** [inlined]

 [3] **read_heap_object(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.GlobalHeapID, ::JLD2.ReadRepresentation{UInt8,UInt8} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/global_heaps.jl:130**

 [4] **jlconvert** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/data.jl:700** [inlined]

 [5] **jlconvert** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/data.jl:766** [inlined]

 [6] **macro expansion** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/dataio.jl:70** [inlined]

 [7] **macro expansion** at **./simdloop.jl:73** [inlined]

 [8] **read_array!** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/dataio.jl:68** [inlined]

 [9] **read_array(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadDataspace, ::JLD2.ReadRepresentation{String,JLD2.Vlen{String}}, ::Int64, ::UInt16, ::JLD2.RelOffset, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:323**

 [10] **read_data(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadRepresentation{String,JLD2.Vlen{String}}, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:173**

 [11] **macro expansion** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datatypes.jl:76** [inlined]

 [12] **read_data(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadDataspace, ::UInt8, ::Int64, ::Int64, ::Int64, ::UInt16, ::JLD2.RelOffset, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:152**

 [13] **load_dataset(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.RelOffset **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:92**

 [14] **jlconvert** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/data.jl:674** [inlined]

 [15] **macro expansion** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/dataio.jl:70** [inlined]

 [16] **macro expansion** at **./simdloop.jl:73** [inlined]

 [17] **read_array!** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/dataio.jl:68** [inlined]

 [18] **read_array(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadDataspace, ::JLD2.ReadRepresentation{AbstractArray{T,1} where T,JLD2.RelOffset}, ::Int64, ::UInt16, ::JLD2.RelOffset, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:323**

 [19] **macro expansion** at **./logging.jl:309** [inlined]

 [20] **read_data(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadRepresentation{Any,JLD2.RelOffset}, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:194**

 [21] **macro expansion** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:154** [inlined] (repeats 2 times)

 [22] **macro expansion** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datatypes.jl:72** [inlined]

 [23] **read_data(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadDataspace, ::UInt8, ::Int64, ::Int64, ::Int64, ::UInt16, ::JLD2.RelOffset, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:152**

 [24] **load_dataset(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.RelOffset **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:92**

 [25] **jlconvert** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/data.jl:674** [inlined]

 [26] **macro expansion** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/data.jl:1285** [inlined]

 [27] **jlconvert(** ::JLD2.ReadRepresentation{getfield(JLD2.ReconstructedTypes, Symbol("##DataFrames.DataFrame#373")),JLD2.OnDiskRepresentation{(0, 8),Tuple{Any,getfield(JLD2.ReconstructedTypes, Symbol("##DataFrames.Index#372"))},Tuple{JLD2.RelOffset,JLD2.OnDiskRepresentation{(0, 8),Tuple{Dict{Symbol,Int64},Any},Tuple{JLD2.CustomSerialization{Array,JLD2.RelOffset},JLD2.RelOffset}}()}}()}, ::JLD2.JLDFile{JLD2.MmapIO}, ::Ptr{Nothing}, ::JLD2.RelOffset **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/data.jl:1232**

 [28] **read_data(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadRepresentation{getfield(JLD2.ReconstructedTypes, Symbol("##DataFrames.DataFrame#373")),JLD2.OnDiskRepresentation{(0, 8),Tuple{Any,getfield(JLD2.ReconstructedTypes, Symbol("##DataFrames.Index#372"))},Tuple{JLD2.RelOffset,JLD2.OnDiskRepresentation{(0, 8),Tuple{Dict{Symbol,Int64},Any},Tuple{JLD2.CustomSerialization{Array,JLD2.RelOffset},JLD2.RelOffset}}()}}()}, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/dataio.jl:37**

 [29] **read_data(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.ReadDataspace, ::UInt8, ::Int64, ::Int64, ::Int64, ::UInt16, ::JLD2.RelOffset, ::Array{JLD2.ReadAttribute,1} **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:149**

 [30] **load_dataset(** ::JLD2.JLDFile{JLD2.MmapIO}, ::JLD2.RelOffset **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/datasets.jl:92**

 [31] **getindex(** ::JLD2.Group{JLD2.JLDFile{JLD2.MmapIO}}, ::String **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/groups.jl:108**

 [32] **read(** ::JLD2.JLDFile{JLD2.MmapIO}, ::String **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/JLD2.jl:326**

 [33] **#3** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/loadsave.jl:77** [inlined]

 [34] **#jldopen#31(** ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::getfield(Main, Symbol("##3#4")), ::String **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/loadsave.jl:4**

 [35] **jldopen(** ::Function, ::String **)** at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/loadsave.jl:2**

 [36] top-level scope at **/groups/scicompsoft/home/arthurb/.julia/packages/JLD2/KjBIK/src/loadsave.jl:76*