Some added modules fail on not loading `lib/julia/sys.so`

Kunz-David · April 17, 2020, 4:31pm

Hello,
I wanted to try out a module I’m working on a fresh installed linux with julia and ran into an error. I first tried to do a simple add module and test, but that failed, so I tried the Example module, which worked, but a random different module failed with a similar issue. Can someone help me solve this issue please?

Code with that I ran:
My module

(@v1.4) pkg> st
Status `~/.julia/environments/v1.4/Project.toml`
  (empty environment)

(@v1.4) pkg> add https://github.com/Kunz-David/LAP_Julia
   Updating git-repo `https://github.com/Kunz-David/LAP_Julia`
  Resolving package versions...
   Updating `~/.julia/environments/v1.4/Project.toml`
  [797d5b5c] + LAP_julia v0.1.0 #master (https://github.com/Kunz-David/LAP_Julia)
   Updating `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] + AbstractFFTs v0.5.0
  [13072b0f] + AxisAlgorithms v1.0.0
  [39de3d68] + AxisArrays v0.4.0
  [336ed68f] + CSV v0.6.1
  [aafaddc9] + CatIndices v0.2.1
  [324d7699] + CategoricalArrays v0.7.7
  [3da002f7] + ColorTypes v0.10.2
  [c3611d14] + ColorVectorSpace v0.8.5
  [5ae59095] + Colors v0.12.0
  [34da2185] + Compat v3.8.0
  [e66e0078] + CompilerSupportLibraries_jll v0.3.3+0
  [ed09eef8] + ComputationalResources v0.3.2
  [8f4d0f93] + Conda v1.4.1
  [150eb455] + CoordinateTransformations v0.5.1
  [dc8bdbbb] + CustomUnitRanges v1.0.0
  [9a962f9c] + DataAPI v1.1.0
  [a93c6f00] + DataFrames v0.20.2
  [864edb3b] + DataStructures v0.17.12
  [e2d170a0] + DataValueInterfaces v1.0.0
  [b4f34e82] + Distances v0.8.2
  [da5c29d0] + EllipsisNotation v0.4.0
  [4f61f5a4] + FFTViews v0.3.1
  [7a1cc6ca] + FFTW v1.2.0
  [f5851436] + FFTW_jll v3.3.9+5
  [5789e2e9] + FileIO v1.2.4
  [48062228] + FilePathsBase v0.7.0
  [53c48c17] + FixedPointNumbers v0.8.0
  [a2bd30eb] + Graphics v1.0.2
  [bbac6d45] + IdentityRanges v0.3.1
  [2803e5a7] + ImageAxes v0.6.4
  [f332f351] + ImageContrastAdjustment v0.3.5
  [a09fc81d] + ImageCore v0.8.14
  [51556ac3] + ImageDistances v0.2.7
  [6a3955dd] + ImageFiltering v0.6.11
  [6218d12a] + ImageMagick v1.1.4
  [c73af94c] + ImageMagick_jll v6.9.10-12+1
  [bc367c6b] + ImageMetadata v0.9.1
  [787d08f9] + ImageMorphology v0.2.5
  [2996bd0c] + ImageQualityIndexes v0.1.4
  [4e3cecfd] + ImageShow v0.2.3
  [02fcd773] + ImageTransformations v0.8.4
  [916415d5] + Images v0.22.2
  [9b13fd28] + IndirectArrays v0.5.1
  [1d5cc7b8] + IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] + Interpolations v0.12.9
  [8197267c] + IntervalSets v0.5.0
  [41ab1584] + InvertedIndices v1.0.0
  [c8e1da08] + IterTools v1.3.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [682c06a0] + JSON v0.21.0
  [aacddb02] + JpegTurbo_jll v2.0.1+0
  [797d5b5c] + LAP_julia v0.1.0 #master (https://github.com/Kunz-David/LAP_Julia)
  [b964fa9f] + LaTeXStrings v1.1.0
  [89763e89] + Libtiff_jll v4.0.10+1
  [856f044c] + MKL_jll v2019.0.117+2
  [1914dd2f] + MacroTools v0.5.5
  [dbb5928d] + MappedArrays v0.2.2
  [e1d29d7a] + Missings v0.4.3
  [e94cdb99] + MosaicViews v0.2.2
  [77ba4419] + NaNMath v0.3.3
  [6fe1bfb0] + OffsetArrays v1.0.4
  [efe28fd5] + OpenSpecFun_jll v0.5.3+3
  [bac558e1] + OrderedCollections v1.1.0
  [5432bcbf] + PaddedViews v0.5.4
  [d96e819e] + Parameters v0.12.0
  [69de0a69] + Parsers v1.0.1
  [2dfb63ee] + PooledArrays v0.5.3
  [438e738f] + PyCall v1.91.4
  [d330b81b] + PyPlot v2.9.0
  [dca85d43] + QuartzImageIO v0.6.0
  [b3c3ace0] + RangeArrays v0.3.2
  [c84ed2f1] + Ratios v0.4.0
  [189a3867] + Reexport v0.2.0
  [ae029012] + Requires v1.0.1
  [6038ab10] + Rotations v0.13.0
  [699a6c99] + SimpleTraits v0.9.1
  [a2af1166] + SortingAlgorithms v0.3.1
  [276daf66] + SpecialFunctions v0.10.0
  [90137ffa] + StaticArrays v0.12.1
  [2913bbd2] + StatsBase v0.33.0
  [3783bdb8] + TableTraits v1.0.0
  [bd369af6] + Tables v1.0.4
  [5e47fb64] + TestImages v1.0.2
  [06e1c1a7] + TiledIteration v0.2.4
  [81def892] + VersionParsing v1.2.0
  [ea10d353] + WeakRefStrings v0.6.2
  [efce3f68] + WoodburyMatrices v0.5.2
  [a5390f91] + ZipFile v0.9.1
  [83775a58] + Zlib_jll v1.2.11+9
  [3161d3a3] + Zstd_jll v1.4.4+0
  [b53b4c65] + libpng_jll v1.6.37+3
  [2a0f44e3] + Base64 
  [ade2ca70] + Dates 
  [8bb1440f] + DelimitedFiles 
  [8ba89e20] + Distributed 
  [9fa8497b] + Future 
  [b77e0a4c] + InteractiveUtils 
  [76f85450] + LibGit2 
  [8f399da3] + Libdl 
  [37e2e46d] + LinearAlgebra 
  [56ddb016] + Logging 
  [d6f4376e] + Markdown 
  [a63ad114] + Mmap 
  [44cfe95a] + Pkg 
  [de0858da] + Printf 
  [3fa0cd96] + REPL 
  [9a3f8284] + Random 
  [ea8e919c] + SHA 
  [9e88b42a] + Serialization 
  [1a1011a3] + SharedArrays 
  [6462fe0b] + Sockets 
  [2f01184e] + SparseArrays 
  [10745b16] + Statistics 
  [8dfed614] + Test 
  [cf7118a7] + UUIDs 
  [4ec0a83e] + Unicode 

(@v1.4) pkg> test LAP_julia
    Testing LAP_julia
Status `/tmp/jl_Pmakcz/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.4.0
  [336ed68f] CSV v0.6.1
  [aafaddc9] CatIndices v0.2.1
  [324d7699] CategoricalArrays v0.7.7
  [3da002f7] ColorTypes v0.10.2
  [c3611d14] ColorVectorSpace v0.8.5
  [5ae59095] Colors v0.12.0
  [34da2185] Compat v3.8.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.3+0
  [ed09eef8] ComputationalResources v0.3.2
  [8f4d0f93] Conda v1.4.1
  [150eb455] CoordinateTransformations v0.5.1
  [dc8bdbbb] CustomUnitRanges v1.0.0
  [9a962f9c] DataAPI v1.1.0
  [a93c6f00] DataFrames v0.20.2
  [864edb3b] DataStructures v0.17.12
  [e2d170a0] DataValueInterfaces v1.0.0
  [b4f34e82] Distances v0.8.2
  [da5c29d0] EllipsisNotation v0.4.0
  [4f61f5a4] FFTViews v0.3.1
  [7a1cc6ca] FFTW v1.2.0
  [f5851436] FFTW_jll v3.3.9+5
  [5789e2e9] FileIO v1.2.4
  [48062228] FilePathsBase v0.7.0
  [53c48c17] FixedPointNumbers v0.8.0
  [a2bd30eb] Graphics v1.0.2
  [bbac6d45] IdentityRanges v0.3.1
  [2803e5a7] ImageAxes v0.6.4
  [f332f351] ImageContrastAdjustment v0.3.5
  [a09fc81d] ImageCore v0.8.14
  [51556ac3] ImageDistances v0.2.7
  [6a3955dd] ImageFiltering v0.6.11
  [6218d12a] ImageMagick v1.1.4
  [c73af94c] ImageMagick_jll v6.9.10-12+1
  [bc367c6b] ImageMetadata v0.9.1
  [787d08f9] ImageMorphology v0.2.5
  [2996bd0c] ImageQualityIndexes v0.1.4
  [4e3cecfd] ImageShow v0.2.3
  [02fcd773] ImageTransformations v0.8.4
  [916415d5] Images v0.22.2
  [9b13fd28] IndirectArrays v0.5.1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] Interpolations v0.12.9
  [8197267c] IntervalSets v0.5.0
  [41ab1584] InvertedIndices v1.0.0
  [c8e1da08] IterTools v1.3.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [682c06a0] JSON v0.21.0
  [aacddb02] JpegTurbo_jll v2.0.1+0
  [797d5b5c] LAP_julia v0.1.0 #master (https://github.com/Kunz-David/LAP_Julia)
  [b964fa9f] LaTeXStrings v1.1.0
  [89763e89] Libtiff_jll v4.0.10+1
  [856f044c] MKL_jll v2019.0.117+2
  [1914dd2f] MacroTools v0.5.5
  [dbb5928d] MappedArrays v0.2.2
  [e1d29d7a] Missings v0.4.3
  [e94cdb99] MosaicViews v0.2.2
  [77ba4419] NaNMath v0.3.3
  [6fe1bfb0] OffsetArrays v1.0.4
  [efe28fd5] OpenSpecFun_jll v0.5.3+3
  [bac558e1] OrderedCollections v1.1.0
  [5432bcbf] PaddedViews v0.5.4
  [d96e819e] Parameters v0.12.0
  [69de0a69] Parsers v1.0.1
  [2dfb63ee] PooledArrays v0.5.3
  [438e738f] PyCall v1.91.4
  [d330b81b] PyPlot v2.9.0
  [dca85d43] QuartzImageIO v0.6.0
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.4.0
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.0.1
  [6038ab10] Rotations v0.13.0
  [699a6c99] SimpleTraits v0.9.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.10.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.33.0
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v1.0.4
  [5e47fb64] TestImages v1.0.2
  [06e1c1a7] TiledIteration v0.2.4
  [81def892] VersionParsing v1.2.0
  [ea10d353] WeakRefStrings v0.6.2
  [efce3f68] WoodburyMatrices v0.5.2
  [a5390f91] ZipFile v0.9.1
  [83775a58] Zlib_jll v1.2.11+9
  [3161d3a3] Zstd_jll v1.4.4+0
  [b53b4c65] libpng_jll v1.6.37+3
  [2a0f44e3] Base64 
  [ade2ca70] Dates 
  [8bb1440f] DelimitedFiles 
  [8ba89e20] Distributed 
  [9fa8497b] Future 
  [b77e0a4c] InteractiveUtils 
  [76f85450] LibGit2 
  [8f399da3] Libdl 
  [37e2e46d] LinearAlgebra 
  [56ddb016] Logging 
  [d6f4376e] Markdown 
  [a63ad114] Mmap 
  [44cfe95a] Pkg 
  [de0858da] Printf 
  [3fa0cd96] REPL 
  [9a3f8284] Random 
  [ea8e919c] SHA 
  [9e88b42a] Serialization 
  [1a1011a3] SharedArrays 
  [6462fe0b] Sockets 
  [2f01184e] SparseArrays 
  [10745b16] Statistics 
  [8dfed614] Test 
  [cf7118a7] UUIDs 
  [4ec0a83e] Unicode 
ERROR: could not load library "/usr/local/julia-1.4.0/lib/julia/sys.so"
/usr/local/julia-1.4.0/lib/julia/sys.so: failed to map segment from shared object
ERROR: LoadError: Failed to precompile MosaicViews [e94cdb99-869f-56ef-bcf0-1ae2bcbe0389] to /home/parallels/.julia/compiled/v1.4/MosaicViews/X3bJX_48GfL.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/parallels/.julia/packages/ImageCore/13hYe/src/ImageCore.jl:19
ERROR: LoadError: Failed to precompile ImageCore [a09fc81d-aa75-5fe9-8630-4744c3626534] to /home/parallels/.julia/compiled/v1.4/ImageCore/cqNLm_48GfL.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/parallels/.julia/packages/ImageFiltering/jhBno/src/ImageFiltering.jl:4
ERROR: LoadError: LoadError: Failed to precompile ImageFiltering [6a3955dd-da59-5b1f-98d4-e7296123deb5] to /home/parallels/.julia/compiled/v1.4/ImageFiltering/MN5uU_48GfL.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] include(::String) at /home/parallels/.julia/packages/LAP_julia/c4vTV/src/LAP_julia.jl:2
 [8] top-level scope at /home/parallels/.julia/packages/LAP_julia/c4vTV/src/LAP_julia.jl:4
 [9] include(::Module, ::String) at ./Base.jl:377
 [10] top-level scope at none:2
 [11] eval at ./boot.jl:331 [inlined]
 [12] eval(::Expr) at ./client.jl:449
 [13] top-level scope at ./none:3
in expression starting at /home/parallels/.julia/packages/LAP_julia/c4vTV/src/helpers.jl:3
in expression starting at /home/parallels/.julia/packages/LAP_julia/c4vTV/src/LAP_julia.jl:4
ERROR: LoadError: Failed to precompile LAP_julia [797d5b5c-2e9a-429f-9c9f-727808915e33] to /home/parallels/.julia/compiled/v1.4/LAP_julia/63ZMV_48GfL.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::String) at ./client.jl:439
 [7] top-level scope at none:6
in expression starting at /home/parallels/.julia/packages/LAP_julia/c4vTV/test/runtests.jl:2
ERROR: Package LAP_julia errored during testing

Example

(@v1.4) pkg> add Example
  Resolving package versions...
   Updating `~/.julia/environments/v1.4/Project.toml`
  [7876af07] + Example v0.5.3
   Updating `~/.julia/environments/v1.4/Manifest.toml`
  [7876af07] + Example v0.5.3

(@v1.4) pkg> test Example
    Testing Example
Status `/tmp/jl_YbL6Zr/Manifest.toml`
  [7876af07] Example v0.5.3
  [2a0f44e3] Base64 
  [8ba89e20] Distributed 
  [b77e0a4c] InteractiveUtils 
  [56ddb016] Logging 
  [d6f4376e] Markdown 
  [9a3f8284] Random 
  [9e88b42a] Serialization 
  [6462fe0b] Sockets 
  [8dfed614] Test 
    Testing Example tests passed

Augmentor

(@v1.4) pkg> add Augmentor
  Resolving package versions...
   Updating `~/.julia/environments/v1.4/Project.toml`
  [02898b10] + Augmentor v0.6.0
   Updating `~/.julia/environments/v1.4/Manifest.toml`
  [02898b10] + Augmentor v0.6.0
  [7f8f8fb0] + LearnBase v0.3.0
  [9920b226] + MLDataPattern v0.5.1
  [66a33bbf] + MLLabelUtils v0.5.2
  [6fe1bfb0] ↓ OffsetArrays v1.0.4 ⇒ v0.11.4

(@v1.4) pkg> test Augmentor
    Testing Augmentor
Status `/tmp/jl_2taeD7/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [02898b10] Augmentor v0.6.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.4.0
  [aafaddc9] CatIndices v0.2.1
  [3da002f7] ColorTypes v0.10.2
  [c3611d14] ColorVectorSpace v0.8.5
  [5ae59095] Colors v0.12.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.3+0
  [ed09eef8] ComputationalResources v0.3.2
  [150eb455] CoordinateTransformations v0.5.1
  [a8cc5b0e] Crayons v4.0.1
  [dc8bdbbb] CustomUnitRanges v1.0.0
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.12
  [ab62b9b5] DeepDiffs v1.2.0
  [b4f34e82] Distances v0.8.2
  [da5c29d0] EllipsisNotation v0.4.0
  [4f61f5a4] FFTViews v0.3.1
  [7a1cc6ca] FFTW v1.2.0
  [f5851436] FFTW_jll v3.3.9+5
  [5789e2e9] FileIO v1.2.4
  [53c48c17] FixedPointNumbers v0.8.0
  [a2bd30eb] Graphics v1.0.2
  [bbac6d45] IdentityRanges v0.3.1
  [2803e5a7] ImageAxes v0.6.4
  [a09fc81d] ImageCore v0.8.14
  [51556ac3] ImageDistances v0.2.7
  [6a3955dd] ImageFiltering v0.6.11
  [d8c32880] ImageInTerminal v0.4.3
  [6218d12a] ImageMagick v1.1.4
  [c73af94c] ImageMagick_jll v6.9.10-12+1
  [bc367c6b] ImageMetadata v0.9.1
  [02fcd773] ImageTransformations v0.8.4
  [9b13fd28] IndirectArrays v0.5.1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] Interpolations v0.12.9
  [8197267c] IntervalSets v0.5.0
  [c8e1da08] IterTools v1.3.0
  [aacddb02] JpegTurbo_jll v2.0.1+0
  [7f8f8fb0] LearnBase v0.3.0
  [89763e89] Libtiff_jll v4.0.10+1
  [856f044c] MKL_jll v2019.0.117+2
  [9920b226] MLDataPattern v0.5.1
  [66a33bbf] MLLabelUtils v0.5.2
  [1914dd2f] MacroTools v0.5.5
  [dbb5928d] MappedArrays v0.2.2
  [e1d29d7a] Missings v0.4.3
  [e94cdb99] MosaicViews v0.2.2
  [77ba4419] NaNMath v0.3.3
  [6fe1bfb0] OffsetArrays v0.11.4
  [efe28fd5] OpenSpecFun_jll v0.5.3+3
  [bac558e1] OrderedCollections v1.1.0
  [5432bcbf] PaddedViews v0.5.4
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.4.0
  [189a3867] Reexport v0.2.0
  [324d217c] ReferenceTests v0.9.0
  [ae029012] Requires v1.0.1
  [6038ab10] Rotations v0.13.0
  [699a6c99] SimpleTraits v0.9.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.10.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.33.0
  [5e47fb64] TestImages v1.0.2
  [06e1c1a7] TiledIteration v0.2.4
  [efce3f68] WoodburyMatrices v0.5.2
  [a5390f91] ZipFile v0.9.1
  [83775a58] Zlib_jll v1.2.11+9
  [3161d3a3] Zstd_jll v1.4.4+0
  [b53b4c65] libpng_jll v1.6.37+3
  [2a0f44e3] Base64 
  [ade2ca70] Dates 
  [8ba89e20] Distributed 
  [b77e0a4c] InteractiveUtils 
  [76f85450] LibGit2 
  [8f399da3] Libdl 
  [37e2e46d] LinearAlgebra 
  [56ddb016] Logging 
  [d6f4376e] Markdown 
  [a63ad114] Mmap 
  [44cfe95a] Pkg 
  [de0858da] Printf 
  [3fa0cd96] REPL 
  [9a3f8284] Random 
  [ea8e919c] SHA 
  [9e88b42a] Serialization 
  [1a1011a3] SharedArrays 
  [6462fe0b] Sockets 
  [2f01184e] SparseArrays 
  [10745b16] Statistics 
  [8dfed614] Test 
  [cf7118a7] UUIDs 
  [4ec0a83e] Unicode 
ERROR: could not load library "/usr/local/julia-1.4.0/lib/julia/sys.so"
/usr/local/julia-1.4.0/lib/julia/sys.so: failed to map segment from shared object
ERROR: LoadError: Failed to precompile OffsetArrays [6fe1bfb0-de20-5000-8ca7-80f57d26f881] to /home/parallels/.julia/compiled/v1.4/OffsetArrays/UDEDl_ZFPk7.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/parallels/.julia/packages/PaddedViews/uoA7B/src/PaddedViews.jl:3
ERROR: LoadError: Failed to precompile PaddedViews [5432bcbf-9aad-5242-b902-cca2824c8663] to /home/parallels/.julia/compiled/v1.4/PaddedViews/SrUyA_ZFPk7.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/parallels/.julia/packages/MosaicViews/AvyaR/src/MosaicViews.jl:3
ERROR: LoadError: Failed to precompile MosaicViews [e94cdb99-869f-56ef-bcf0-1ae2bcbe0389] to /home/parallels/.julia/compiled/v1.4/MosaicViews/X3bJX_ZFPk7.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/parallels/.julia/packages/ImageCore/13hYe/src/ImageCore.jl:19
ERROR: LoadError: Failed to precompile ImageCore [a09fc81d-aa75-5fe9-8630-4744c3626534] to /home/parallels/.julia/compiled/v1.4/ImageCore/cqNLm_ZFPk7.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::String) at ./client.jl:439
 [7] top-level scope at none:6
in expression starting at /home/parallels/.julia/packages/Augmentor/kkcKe/test/runtests.jl:1
ERROR: Package Augmentor errored during testing

This are my versioninfo():

julia> versioninfo()
Julia Version 1.4.0
Commit b8e9a9ecc6 (2020-03-21 16:36 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i5-4288U CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.1 (ORCJIT, haswell)

Kunz-David · April 18, 2020, 8:34am

So I tried to do the same on another MacOS machine and my module worked, so think the problem has something to do with the using linux.

pixel27 · April 18, 2020, 6:43pm

Make sure /usr/local/julia-1.4.0/lib/julia/sys.so exists.
Make sure the permissions on /usr/local/julia-1.4.0/lib/julia/sys.so allow you to read and execute it.
If you run which julia does it show /usr/local/bin/julia? Or something else?
This would be a long shot but in there a julia file under /usr/local/julia-1.4.0/bin? If there is what if you execute that instance of julia (assuming it’s different that what you found in #3)?

Kunz-David · April 18, 2020, 7:25pm

Thanks for the answer.

I tried to install julia 1.4.1 to see if it will solve the issue (it did’t), so I’m answering for the new julia.

Make sure /usr/local/julia-1.4.0/lib/julia/sys.so exists.

It does

Make sure the permissions on /usr/local/julia-1.4.0/lib/julia/sys.so allow you to read and execute it.

I do have permissions to read and execute (I have -rwxr-xr-x).
I tried to run it and it gives a seg fault, but that might be alright? I don’t know.

If you run which julia does it show /usr/local/bin/julia ? Or something else?

It returns: /usr/local/julia-1.4.1/bin/julia.

This would be a long shot but in there a julia file under /usr/local/julia-1.4.0/bin ? If there is what if you execute that instance of julia (assuming it’s different that what you found in #3)?

There is a julia executable file and it’s the same as from which julia.

No leads from this I’m afraid.

pixel27 · April 18, 2020, 8:10pm

Yeah, I really don’t know where to go from here. What distro are you using?

Kunz-David · April 18, 2020, 9:41pm

I’m running ubuntu 16.04 LTS.

pixel27 · April 18, 2020, 10:37pm

Well you will be unhappy to know that I can’t reproduce the issue. I installed Ubuntu 16.04 into virtualbox:

Linux version 4.4.0-177-generic (buildd@lgw01-amd64-035) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.12) ) #207-Ubuntu SMP Mon Mar 16 01:16:10 UTC 2020

Downloaded the official Julia binaries for 1.4.1.
Extracted the files, moved the whole directory to /usr/local (I didn’t change the owner, so the owner is me, did you change the owner to root or something?).
Added export PATH=$PATH:/usr/local/julia-1.4.1/bin to my .bashrc.

And was able to add the the https://github.com/Kunz-David/LAP_Julia and test it without issue (once I installed a python3 package).

Hello             World!
Test Summary: | Pass  Total
helpers       |  162    162
Test Summary: | Pass  Total
inpaint       |    2      2
    Testing LAP_julia tests passed

Six of the Augmentor tests fail:

Test Summary:              | Pass  Fail  Total
operations/tst_channels.jl |  742     2    744
  SplitChannels            |  313          313
  CombineChannels          |  429     2    431
    constructor            |    6     2      8
    eager                  |  151          151
    affine                 |    1            1
    affineview             |    1            1
    lazy                   |  264          264
    view                   |    1            1
    stepview               |    1            1
    permute                |    1            1

But I didn’t get a mapping issue.

Kunz-David · April 19, 2020, 10:31am

Wow, well I went through exactly the same steps. The olny difference I see is that my ubuntu is installed on parallels desktop. But I don’t know if that can even play a role in causing this issue.
Anyway thanks for the help and effort, I’ll post here if I get find out what’s going on.

pixel27 · April 19, 2020, 11:20am

Someone just posted here. The post was basically experiencing the same “failed to map segment from shared object” for sys.so during precompilation. Basically they had a lack of memory. When I did my virtualbox test it was with 4gb in the VM.

I was able to reproduce your problem when I dropped the RAM down to 1GB with 1GB of swap space…so my guess would be you need more memory.

Kunz-David · April 19, 2020, 12:48pm

Yes, this was the issue! I had 1GB of RAM, setting it to 2GB did the trick. Thanks for your help!