Error Read File after package update

General Usage
, ,
1

Hi,
after
Pkg.update() in Julia v1.3.1
I had issues during recompiling of whichever package,
for example:

Precompiling Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]
ERROR: LoadError: EOFError: read end of file
Stacktrace:
 [1] read(::IOStream, ::Type{Int64}) at ./iostream.jl:361
 [2] parse_cache_header(::IOStream) at ./loading.jl:1334
 [3] stale_cachefile(::String, ::String) at ./loading.jl:1413
 [4] _require_search_from_serialized(::Base.PkgId, ::String) at ./loading.jl:752
 [5] _tryrequire_from_serialized(::Base.PkgId, ::UInt64, ::String) at ./loading.jl:707
 [6] _require_search_from_serialized(::Base.PkgId, ::String) at ./loading.jl:765
 [7] _tryrequire_from_serialized(::Base.PkgId, ::UInt64, ::String) at ./loading.jl:707
 [8] _require_search_from_serialized(::Base.PkgId, ::String) at ./loading.jl:765
 [9] _require(::Base.PkgId) at ./loading.jl:1001
 [10] require(::Base.PkgId) at ./loading.jl:922
 [11] require(::Module, ::Symbol) at ./loading.jl:917
 [12] include at ./boot.jl:328 [inlined]
 [13] include_relative(::Module, ::String) at ./loading.jl:1105
 [14] include(::Module, ::String) at ./Base.jl:31
 [15] top-level scope at none:2
 [16] eval at ./boot.jl:330 [inlined]
 [17] eval(::Expr) at ./client.jl:425
 [18] top-level scope at ./none:3
in expression starting at /usr/local/share/julia/home/packages/Plots/qZHsp/src/Plots.jl:19
ERROR: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to /usr/local/share/julia/home/compiled/v1.3/Plots/ld3vC_5tSes.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1283
 [3] _require(::Base.PkgId) at ./loading.jl:1024
 [4] require(::Base.PkgId) at ./loading.jl:922
 [5] require(::Module, ::Symbol) at ./loading.jl:917

My packages are:

  [c52e3926] Atom v0.11.3
  [6e4b80f9] BenchmarkTools v0.4.3
  [159f3aea] Cairo v1.0.2
  [5ae59095] Colors v0.10.2
  [a93c6f00] DataFrames v0.20.0
  [1313f7d8] DataFramesMeta v0.5.0
  [864edb3b] DataStructures v0.17.9
  [01453d9d] DiffEqDiffTools v1.7.0
  [0c46a032] DifferentialEquations v6.10.1
  [31c24e10] Distributions v0.21.12
  [c91e804a] Gadfly v1.0.1
  [f67ccb44] HDF5 v0.12.5
  [4138dd39] JLD v0.9.1
  [e5e0dc1b] Juno v0.7.2
  [b964fa9f] LaTeXStrings v1.0.3
  [23fbe1c1] Latexify v0.12.3
  [2fda8390] LsqFit v0.10.0
  [eff96d63] Measurements v2.1.1
  [6f286f6a] MultivariateStats v0.7.0
  [f853b5e0] Pandoc v0.2.5
  [d96e819e] Parameters v0.12.0
  [91a5bcdd] Plots v0.28.4
  [08abe8d2] PrettyTables v0.6.0
  [438e738f] PyCall v1.91.2
  [d330b81b] PyPlot v2.8.2
  [1fd47b50] QuadGK v2.3.1
  [ce6b1742] RDatasets v0.6.6
  [60ddc479] StatPlots v0.9.2
  [2913bbd2] StatsBase v0.32.0
  [44d3d7a6] Weave v0.9.1

Thanks,
Alessio

2

Seems like there is a corrupt file somewhere in your depot. You could try deleting the directory at ~/.julia/compiled/v1.3

1 Like
4

I have some issue with compiling Plots.

at the beginning I had the same error
ERROR: LoadError: EOFError: read end of file

I removed the directory ~/.julia/compiled/v1.3, as suggested, but now I get these errors:

┌ Info: Precompiling Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]
â”” @ Base loading.jl:1273

signal (11): Segmentation fault: 11
in expression starting at none:0
jl_is_submodule at /Users/sabae/buildbot/worker/package_macos64/build/src/module.c:765
module_in_worklist at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:227 [inlined]
type_in_worklist at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:238
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:987
jl_serialize_module at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:447 [inlined]
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:904
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:687
jl_save_incremental at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:2832
jl_write_compiler_output at /Users/sabae/buildbot/worker/package_macos64/build/src/precompile.c:66
jl_atexit_hook at /Users/sabae/buildbot/worker/package_macos64/build/src/init.c:230
main at /Applications/Julia-1.3.app/Contents/Resources/julia/bin/julia (unknown line)
Allocations: 6510452 (Pool: 6509687; Big: 765); GC: 5
ERROR: LoadError: Failed to precompile GeometryBasics [5c1252a2-5f33-56bf-86c9-59e7332b4326] to /Users/roi/.julia/compiled/v1.3/GeometryBasics/lB452_lObFt.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1283
 [3] _require(::Base.PkgId) at ./loading.jl:1024
 [4] require(::Base.PkgId) at ./loading.jl:922
 [5] require(::Module, ::Symbol) at ./loading.jl:917
 [6] include at ./boot.jl:328 [inlined]
 [7] include_relative(::Module, ::String) at ./loading.jl:1105
 [8] include(::Module, ::String) at ./Base.jl:31
 [9] top-level scope at none:2
 [10] eval at ./boot.jl:330 [inlined]
 [11] eval(::Expr) at ./client.jl:425
 [12] top-level scope at ./none:3
in expression starting at /Users/roi/.julia/packages/Plots/mXrnb/src/Plots.jl:11

Do you know what could be the problem?

5

I’m getting the same error. I deleted my ~/.julia directory to start fresh and I still can’t compile GeometryBasics

using Plots
[ Info: Precompiling Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]

signal (11): Segmentation fault: 11
in expression starting at none:0
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:589
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:1016
jl_serialize_module at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:447 [inlined]
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:904
jl_serialize_value_ at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:687
jl_save_incremental at /Users/sabae/buildbot/worker/package_macos64/build/src/dump.c:2832
jl_write_compiler_output at /Users/sabae/buildbot/worker/package_macos64/build/src/precompile.c:66
jl_atexit_hook at /Users/sabae/buildbot/worker/package_macos64/build/src/init.c:230
main at /Applications/Julia-1.3.app/Contents/Resources/julia/bin/julia (unknown line)
Allocations: 6475594 (Pool: 6474830; Big: 764); GC: 4
ERROR: LoadError: Failed to precompile GeometryBasics [5c1252a2-5f33-56bf-86c9-59e7332b4326] to
6

Same problem here

7

I thought to myself: “An opportunity to test Makie”. The thing is, Makie also depends on GeometryBasics (which now seems obvious). :scream: :sob:

8

Same problem here, any solution found? (deleting the compiled directory didn’t work). I just moved on to a different Julia version (I was using 1.3).