Pkg: status/instantiate: "ERROR: IOError: stat: permission denied (EACCES)"

When I do ] status or ] instantiate inside a folder with a Project.toml and a Manifest.toml file, I get the error:

ERROR: IOError: stat: permission denied (EACCES)

Here is the full shell output:

omlins@daint106:/scratch/snx3000/omlins/36693/reproduce> rm -rf ~/.julia
omlins@daint106:/scratch/snx3000/omlins/36693/reproduce> julia
(v1.1) pkg> activate .

julia> status
ERROR: UndefVarError: status not defined

(reproduce) pkg> status
    Status `/scratch/snx3000/omlins/36693/reproduce/Project.toml`
→ [c7e460c6] ArgParse v0.6.2
→ [8f4d0f93] Conda v1.3.0
→ [55939f99] DecFP v0.4.8
→ [c27321d9] Glob v1.2.0
ERROR: IOError: stat: permission denied (EACCES)
Stacktrace:
 [1] stat(::String) at ./stat.jl:68
 [2] isfile at ./stat.jl:303 [inlined]
 [3] isfile_casesensitive at ./loading.jl:9 [inlined]
 [4] entry_path(::String, ::String) at ./loading.jl:420
 [5] (::getfield(Base, Symbol("##657#658")){String,Base.PkgId})(::IOStream) at ./loading.jl:539
 [6] #open#310(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::getfield(Base, Symbol("##657#658")){String,Base.PkgId}, ::String) at ./iostream.jl:369
 [7] open at ./iostream.jl:367 [inlined]
 [8] explicit_manifest_uuid_path at ./loading.jl:520 [inlined]
 [9] manifest_uuid_path(::String, ::Base.PkgId) at ./loading.jl:324
 [10] locate_package(::Base.PkgId) at ./loading.jl:245
 [11] print_diff(::Base.TTY, ::Pkg.Types.Context, ::Array{Pkg.Display.DiffEntry,1}, ::Bool) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Display.jl:170
 [12] print_diff(::Pkg.Types.Context, ::Array{Pkg.Display.DiffEntry,1}, ::Bool) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Display.jl:224
 [13] #status#2(::Pkg.Types.PackageMode, ::Bool, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Display.jl:84
 [14] #status at ./none:0 [inlined]
 [15] #status#70(::Pkg.Types.PackageMode, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:484
 [16] (::getfield(Pkg.API, Symbol("#kw##status")))(::NamedTuple{(:mode,),Tuple{Pkg.Types.PackageMode}}, ::typeof(Pkg.API.status), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at ./none:0
 [17] do_status!(::Dict{Symbol,Any}, ::Array{Pkg.Types.PackageSpec,1}, ::Dict{Symbol,Any}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:603
 [18] #invokelatest#1(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:742
 [19] invokelatest(::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:741
 [20] do_cmd!(::Pkg.REPLMode.PkgCommand, ::REPL.LineEditREPL) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:561
 [21] #do_cmd#30(::Bool, ::Function, ::REPL.LineEditREPL, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:536
 [22] do_cmd at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:532 [inlined]
 [23] (::getfield(Pkg.REPLMode, Symbol("##48#51")){REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:967
 [24] #invokelatest#1 at ./essentials.jl:742 [inlined]
 [25] invokelatest at ./essentials.jl:741 [inlined]
 [26] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/REPL/src/LineEdit.jl:2273
 [27] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/REPL/src/REPL.jl:1035
 [28] run_repl(::REPL.AbstractREPL, ::Any) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/REPL/src/REPL.jl:192
 [29] (::getfield(Base, Symbol("##734#736")){Bool,Bool,Bool,Bool})(::Module) at ./client.jl:362
 [30] #invokelatest#1 at ./essentials.jl:742 [inlined]
 [31] invokelatest at ./essentials.jl:741 [inlined]
 [32] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:346
 [33] exec_options(::Base.JLOptions) at ./client.jl:284
 [34] _start() at ./client.jl:436

(reproduce) pkg> instantiate
   Cloning default registries into `~/.julia`
   Cloning registry from "https://github.com/JuliaRegistries/General.git"
     Added registry `General` to `~/.julia/registries/General`
 Installed PlotThemes ────────────────── v0.3.0
 Installed NaNMath ───────────────────── v0.3.2
 Installed AxisAlgorithms ────────────── v1.0.0
 Installed Widgets ───────────────────── v0.6.1
 Installed DecFP ─────────────────────── v0.4.8
 Installed TextWrap ──────────────────── v0.3.0
 Installed Observables ───────────────── v0.2.3
 Installed MathProgBase ──────────────── v0.7.7
 Installed SortingAlgorithms ─────────── v0.3.1
 Installed Parsers ───────────────────── v0.3.6
 Installed LineSearches ──────────────── v7.0.1
 Installed NearestNeighbors ──────────── v0.4.3
 Installed SpecialFunctions ──────────── v0.7.2
 Installed ForwardDiff ───────────────── v0.10.3
 Installed Colors ────────────────────── v0.9.5
 Installed DataValueInterfaces ───────── v1.0.0
 Installed Interpolations ────────────── v0.12.2
 Installed VersionParsing ────────────── v1.1.3
 Installed ProgressMeter ─────────────── v1.0.0
 Installed FillArrays ────────────────── v0.6.3
 Installed BinaryProvider ────────────── v0.5.6
 Installed CommonSubexpressions ──────── v0.2.0
 Installed JSON ──────────────────────── v0.21.0
 Installed ArrayInterface ────────────── v1.2.1
 Installed Plots ─────────────────────── v0.25.3
 Installed QuadGK ────────────────────── v2.0.3
 Installed Ratios ────────────────────── v0.3.1
 Installed DiffRules ─────────────────── v0.0.10
 Installed Compat ────────────────────── v2.1.0
 Installed PlotUtils ─────────────────── v0.5.8
 Installed Arpack ────────────────────── v0.3.1
 Installed Glob ──────────────────────── v1.2.0
 Installed DataStructures ────────────── v0.17.0
 Installed Reexport ──────────────────── v0.2.0
 Installed StaticArrays ──────────────── v0.11.0
 Installed BinDeps ───────────────────── v0.8.10
 Installed Conda ─────────────────────── v1.3.0
 Installed MathOptInterface ──────────── v0.8.4
 Installed HDF5 ──────────────────────── v0.12.0
 Installed TableTraits ───────────────── v1.0.0
 Installed StatsPlots ────────────────── v0.11.0
 Installed MacroTools ────────────────── v0.5.1
 Installed Showoff ───────────────────── v0.3.1
 Installed Blosc ─────────────────────── v0.5.1
 Installed RecipesBase ───────────────── v0.6.0
 Installed Parameters ────────────────── v0.10.3
 Installed DiffResults ───────────────── v0.0.4
 Installed OffsetArrays ──────────────── v0.11.1
 Installed OrderedCollections ────────── v1.1.0
 Installed CMakeWrapper ──────────────── v0.2.3
 Installed URIParser ─────────────────── v0.4.0
 Installed Requires ──────────────────── v0.5.2
 Installed ColorTypes ────────────────── v0.8.0
 Installed Clustering ────────────────── v0.13.2
 Installed StatsBase ─────────────────── v0.30.0
 Installed Optim ─────────────────────── v0.19.2
 Installed GR ────────────────────────── v0.41.0
 Installed JuMP ──────────────────────── v0.19.2
 Installed PyCall ────────────────────── v1.91.2
 Installed DataAPI ───────────────────── v1.0.1
 Installed PDMats ────────────────────── v0.9.8
 Installed StatsFuns ─────────────────── v0.8.0
 Installed DataValues ────────────────── v0.4.12
 Installed GeometryTypes ─────────────── v0.7.5
 Installed WoodburyMatrices ──────────── v0.4.1
 Installed Rmath ─────────────────────── v0.5.0
 Installed NLSolversBase ─────────────── v7.4.0
 Installed Tokenize ──────────────────── v0.5.5
 Installed Distances ─────────────────── v0.8.0
 Installed IterTools ─────────────────── v1.2.0
 Installed KernelDensity ─────────────── v0.5.1
 Installed Distributions ─────────────── v0.20.0
 Installed Contour ───────────────────── v0.5.1
 Installed DiffEqDiffTools ───────────── v1.3.0
 Installed FFTW ──────────────────────── v0.3.0
 Installed CMake ─────────────────────── v1.1.2
 Installed AbstractFFTs ──────────────── v0.4.1
 Installed Tables ────────────────────── v0.2.10
 Installed CSTParser ─────────────────── v0.6.2
 Installed TickTock ──────────────────── v1.0.0
 Installed PositiveFactorizations ────── v0.2.2
 Installed ArgParse ──────────────────── v0.6.2
 Installed Missings ──────────────────── v0.4.1
 Installed Measures ──────────────────── v0.3.0
 Installed FixedPointNumbers ─────────── v0.6.1
 Installed Ipopt ─────────────────────── v0.5.4
 Installed IteratorInterfaceExtensions ─ v1.0.0
 Installed Calculus ──────────────────── v0.5.0
ERROR: IOError: stat: permission denied (EACCES)
Stacktrace:
 [1] stat(::String) at ./stat.jl:68
 [2] isfile at ./stat.jl:303 [inlined]
 [3] (::getfield(Pkg.Types, Symbol("##30#32")){Tuple{String,String}})(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Types.jl:197
 [4] update_manifest(::Pkg.Types.Context, ::Pkg.Types.PackageSpec, ::Nothing) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:731
 [5] #apply_versions#23(::Symbol, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Dict{Base.UUID,Base.SHA1}, ::Dict{Base.UUID,Array{String,1}}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:652
 [6] apply_versions at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:555 [inlined]
 [7] #instantiate#65(::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:467
 [8] instantiate at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:437 [inlined]
 [9] do_instantiate!(::Dict{Symbol,Any}, ::Array{String,1}, ::Dict{Symbol,Any}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:621
 [10] #invokelatest#1(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:742
 [11] invokelatest(::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:741
 [12] do_cmd!(::Pkg.REPLMode.PkgCommand, ::REPL.LineEditREPL) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:561
 [13] #do_cmd#30(::Bool, ::Function, ::REPL.LineEditREPL, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:536
 [14] do_cmd at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:532 [inlined]
 [15] (::getfield(Pkg.REPLMode, Symbol("##48#51")){REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/REPLMode.jl:967
 [16] #invokelatest#1 at ./essentials.jl:742 [inlined]
 [17] invokelatest at ./essentials.jl:741 [inlined]
 [18] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/REPL/src/LineEdit.jl:2273
 [19] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/REPL/src/REPL.jl:1035
 [20] run_repl(::REPL.AbstractREPL, ::Any) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/REPL/src/REPL.jl:192
 [21] (::getfield(Base, Symbol("##734#736")){Bool,Bool,Bool,Bool})(::Module) at ./client.jl:362
 [22] #invokelatest#1 at ./essentials.jl:742 [inlined]
 [23] invokelatest at ./essentials.jl:741 [inlined]
 [24] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:346
 [25] exec_options(::Base.JLOptions) at ./client.jl:284
 [26] _start() at ./client.jl:436

(reproduce) pkg> 

Note that I get this with Julia v1.1 (shown above) and also with a fresh installation of Julia 1.0.4 and ~/.julia removed before trying.

Can anyone tell me how to fix/debug this?

Thanks!!