Closed mcfefa closed 5 years ago
KristofferC
commented
5 years ago Restarting julia and just executing build should rebuild the packages. Your packages should have been updated by this point. This should be fixed on master which will be in 1.2 julia release.
mcfefa
commented
5 years ago Thanks @KristofferC
It looks like you are right, my packages did update. However there was an error trying to build Cairo, which I'm guessing is what is causing the error MethodError when I try to update. I'll be sure to get the 1.2 julia release to avoid the issue in the future.
MLC02V607JHV2Q:Cancer.jl mcfefa$ julia1.0
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.0.0 (2018-08-08)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(v1.0) pkg> activate .
(Cancer) pkg> build
Building Electron ────────→ `~/.julia/packages/Electron/AHiDq/deps/build.log`
Building LibCURL ─────────→ `~/.julia/packages/LibCURL/khRkY/deps/build.log`
Building WinRPM ──────────→ `~/.julia/packages/WinRPM/Y9QdZ/deps/build.log`
Building Homebrew ────────→ `~/.julia/packages/Homebrew/s09IX/deps/build.log`
Building Cairo ───────────→ `~/.julia/packages/Cairo/CXPG1/deps/build.log`
┌ Error: Error building `Cairo`:
│
│ signal (11): Segmentation fault: 11
│ in expression starting at /Users/mcfefa/.julia/packages/Cairo/CXPG1/deps/build.jl:165
│ _platform_strcmp at /usr/lib/system/libsystem_platform.dylib (unknown line)
│ Allocations: 17996674 (Pool: 17994119; Big: 2555); GC: 40
└ @ Pkg.Operations /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1068
Building Rsvg ────────────→ `~/.julia/packages/Rsvg/uwc9D/deps/build.log`
Building NodeJS ──────────→ `~/.julia/packages/NodeJS/rx0mH/deps/build.log`
Building VegaLite ────────→ `~/.julia/packages/VegaLite/5UYyY/deps/build.log`
Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/fvheQ/deps/build.log`
Building SymEngine ───────→ `~/.julia/packages/SymEngine/6KyFJ/deps/build.log`
Building CodecZlib ───────→ `~/.julia/packages/CodecZlib/9jDi1/deps/build.log`
Building Arpack ──────────→ `~/.julia/packages/Arpack/UiiMc/deps/build.log`
Building Rmath ───────────→ `~/.julia/packages/Rmath/Py9gH/deps/build.log`
Building Conda ───────────→ `~/.julia/packages/Conda/CpuvI/deps/build.log`
Building FFTW ────────────→ `~/.julia/packages/FFTW/p7sLQ/deps/build.log`
Building BlossomV ────────→ `~/.julia/packages/BlossomV/vKHKD/deps/build.log`
Building GLPK ────────────→ `~/.julia/packages/GLPK/rw631/deps/build.log`
Building ZMQ ─────────────→ `~/.julia/packages/ZMQ/ABGOx/deps/build.log`
Building MbedTLS ─────────→ `~/.julia/packages/MbedTLS/X4xar/deps/build.log`
Building IJulia ──────────→ `~/.julia/packages/IJulia/9ajf8/deps/build.log`
Building GR ──────────────→ `~/.julia/packages/GR/IVBgs/deps/build.log`
Building Plots ───────────→ `~/.julia/packages/Plots/QYETN/deps/build.log`
Building Sundials ────────→ `~/.julia/packages/Sundials/eAJ5O/deps/build.log`
Building ZipFile ─────────→ `~/.julia/packages/ZipFile/p60bh/deps/build.log`
Building Dierckx ─────────→ `~/.julia/packages/Dierckx/9SY4A/deps/build.log`
(Cancer) pkg> update
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Updating git-repo `https://github.com/BioJulia/BioSequences.jl.git`
Updating git-repo `https://github.com/JuliaDiffEq/DiffEqTutorials.jl`
Updating git-repo `https://github.com/BioJulia/IntervalTrees.jl.git`
Resolving package versions...
Installed Revise ─ v2.0.2
Updating `Project.toml`
[295af30f] ↑ Revise v2.0.1 ⇒ v2.0.2
Updating `Manifest.toml`
[295af30f] ↑ Revise v2.0.1 ⇒ v2.0.2
ERROR: MethodError: no method matching getindex(::Nothing, ::String)
Stacktrace:
[1] #build_versions#45(::Bool, ::Function, ::Pkg.Types.Context, ::Array{Base.UUID,1}) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1016
[2] build_versions at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1005 [inlined]
[3] up(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1209
[4] #up#31(::Pkg.Types.UpgradeLevel, ::Pkg.Types.PackageMode, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:184
[5] up at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:158 [inlined]
[6] do_up!(::Dict{Symbol,Any}, ::Array{Pkg.Types.PackageSpec,1}, ::Dict{Symbol,Any}) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:610
[7] #invokelatest#1(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:686
[8] invokelatest(::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:685
[9] do_cmd!(::Pkg.REPLMode.PkgCommand, ::REPL.LineEditREPL) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:542
[10] #do_cmd#30(::Bool, ::Function, ::REPL.LineEditREPL, ::String) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:507
[11] do_cmd at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:503 [inlined]
[12] (::getfield(Pkg.REPLMode, Symbol("##41#44")){REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:842
[13] #invokelatest#1 at ./essentials.jl:686 [inlined]
[14] invokelatest at ./essentials.jl:685 [inlined]
[15] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:2261
[16] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:1029
[17] run_repl(::REPL.AbstractREPL, ::Any) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:191
[18] (::getfield(Base, Symbol("##720#722")){Bool,Bool,Bool,Bool})(::Module) at ./logging.jl:311
[19] #invokelatest#1 at ./essentials.jl:686 [inlined]
[20] invokelatest at ./essentials.jl:685 [inlined]
[21] macro expansion at ./logging.jl:308 [inlined]
[22] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:330
[23] exec_options(::Base.JLOptions) at ./client.jl:242
[24] _start() at ./client.jl:421
(Cancer) pkg> Should be fixed
When I try to update my packages using the Pkg manager, I get a MethodError as shown below. Does anyone have a suggestion on what I need to do to fix this?
I've tried this sequence on both v0.7 and v1.0 and it has resulted in the same error message.
resolveruns without error and I've been able to useIJulia, but I don't think my packages are updating appropriately. Any insights on what I may be doing wrong would be greatly appreciated.