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!!