Package evaluation of NeXLParticle on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T13:24:54.370 ################################################################################ # Set-up # Set-up completed after 0.31s ################################################################################ # Installation # Installing NeXLParticle... Resolving package versions... Installed HDF5 ─── v0.16.16 Installed CRlibm ─ v0.8.0 Updating `~/.julia/environments/v1.13/Project.toml` [9f92fee6] + NeXLParticle v0.1.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [621f4979] + AbstractFFTs v1.5.0 [7f219486] + AbstractNFFTs v0.8.2 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.18.0 ⌃ [13072b0f] + AxisAlgorithms v1.0.1 [39de3d68] + AxisArrays v0.4.7 [198e06fe] + BangBang v0.4.4 [9718e550] + Baselet v0.1.1 [26cce99e] + BasicInterpolators v0.7.1 [d1d4a3ce] + BitFlags v0.1.9 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [fe54227b] + BoteSalvatICX v2.0.2 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.6 ⌅ [96374032] + CRlibm v0.8.0 [336ed68f] + CSV v0.10.15 [49dc2e85] + Calculus v0.5.2 [aafaddc9] + CatIndices v0.2.2 [324d7699] + CategoricalArrays v0.10.8 [d360d2e6] + ChainRulesCore v1.25.1 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [944b1d66] + CodecZlib v0.7.8 ⌃ [35d6a980] + ColorSchemes v3.26.0 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [c3611d14] + ColorVectorSpace v0.9.10 ⌅ [5ae59095] + Colors v0.12.11 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a81c6b42] + Compose v0.9.5 [a33af91c] + CompositionsBase v0.1.2 [ed09eef8] + ComputationalResources v0.3.2 [5060bff5] + ConcurrentCollections v0.1.1 [f0e56b4a] + ConcurrentUtilities v2.5.0 [187b0558] + ConstructionBase v1.5.8 [6add18c4] + ContextVariablesX v0.1.3 [150eb455] + CoordinateTransformations v0.6.4 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9c784101] + CubicSplines v0.2.1 [dc8bdbbb] + CustomUnitRanges v1.0.2 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [124859b0] + DataDeps v0.7.13 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [39dd38d3] + Dierckx v0.5.4 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.6.52 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.119 [ffbed154] + DocStringExtensions v0.9.4 [4e289a0a] + EnumX v1.0.5 [90fa49ef] + ErrorfreeArithmetic v0.5.2 [460bff9d] + ExceptionUnwrapping v0.1.11 [e2ba6199] + ExprTools v0.1.10 [411431e0] + Extents v0.1.5 [8f5d6c58] + EzXML v1.2.1 [4f61f5a4] + FFTViews v0.3.2 [7a1cc6ca] + FFTW v1.8.1 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 ⌅ [fa42c844] + FastRounding v0.2.0 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [53c48c17] + FixedPointNumbers v0.8.5 [59287772] + Formatting v0.4.3 ⌅ [f6369f11] + ForwardDiff v0.10.38 [b18b359b] + FourierTools v0.4.8 [68eda718] + GeoFormatTypes v0.4.4 [cf35fbd7] + 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Measures v0.3.2 [c03570c3] + Memoize v0.4.4 ⌅ [626554b9] + MetaGraphs v0.7.2 [128add7d] + MicroCollections v0.2.0 [e1d29d7a] + Missings v1.2.0 [78c3b35d] + Mocking v0.8.1 [e94cdb99] + MosaicViews v0.3.4 ⌅ [98581153] + NDTools v0.7.1 [efe261a4] + NFFT v0.13.7 [d41bc354] + NLSolversBase v7.9.1 [77ba4419] + NaNMath v1.1.3 [71a1bf82] + NameResolution v0.1.5 ⌃ [93a0284f] + NeXLCore v0.3.11 ⌃ [3ab34fdf] + NeXLMatrixCorrection v0.3.9 [9f92fee6] + NeXLParticle v0.1.1 ⌃ [6c578565] + NeXLSpectrum v0.3.6 [7127f3d6] + NeXLUncertainties v0.2.15 [b8a86587] + NearestNeighbors v0.4.21 [f09324ee] + Netpbm v1.1.1 [978898f6] + NumberIntervals v0.2.2 [6fe1bfb0] + OffsetArrays v1.17.0 [a15396b6] + OnlineStats v1.7.1 [925886fa] + OnlineStatsBase v1.7.1 [52e1d378] + OpenEXR v0.3.3 [4d8831e6] + OpenSSL v1.4.3 [429524aa] + Optim v1.12.0 [87e2bd06] + OptimBase v2.0.2 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.34 [f57f5aa1] + PNGFiles v0.4.4 [5432bcbf] + PaddedViews v0.5.12 [d96e819e] + 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SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Building CRlibm → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9d1c22cff9c04207f336b8e64840d0bd40d86e0e/build.log` Building HDF5 ──→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log` Installation completed after 34.46s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... ✗ JLD2 6213.9 ms ✓ Transducers → TransducersOnlineStatsBaseExt 36138.2 ms ✓ NFFT 9547.0 ms ✓ NeXLUncertainties ✗ MetaGraphs 9638.8 ms ✓ FourierTools 131827.0 ms ? NeXLUncertainties → NeXLUncertaintiesDataFramesExt 7181.5 ms ✓ NeXLUncertainties → NeXLUncertaintiesLaTeXStringsExt ✗ ImageSegmentation 133660.2 ms ? NeXLCore ✗ Images 32330.5 ms ? NeXLMatrixCorrection 47719.4 ms ? NeXLSpectrum 71950.1 ms ? NeXLParticle 5 dependencies successfully precompiled in 1194 seconds. 393 already precompiled. 5 dependencies failed but may be precompilable after restarting julia 5 dependencies had output during precompilation: ┌ NeXLCore │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLSpectrum │ WARNING: method definition for IntervalBox at /home/pkgeval/.julia/packages/IntervalArithmetic/dhnJB/src/multidim/intervalbox.jl:21 declares type variable T but does not use it. │ WARNING: method definition for IntervalBox at /home/pkgeval/.julia/packages/IntervalArithmetic/dhnJB/src/multidim/intervalbox.jl:21 declares type variable N but does not use it. │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLMatrixCorrection │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLUncertainties → NeXLUncertaintiesDataFramesExt │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Statistics.cov), SparseArrays.SparseMatrixCSC{Tv, Ti} where Ti<:Integer where Tv) in module SparseArraysExt at /home/pkgeval/.julia/packages/Statistics/gbcbG/ext/SparseArraysExt.jl:14 overwritten in module SparseArraysExt on the same line (check for duplicate calls to `include`). │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLParticle │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ Precompilation completed after 1200.02s ################################################################################ # Loading # Loading NeXLParticle... Precompiling packages... ✗ JLD2 31171.2 ms ? NeXLCore ✗ MetaGraphs 33009.0 ms ? NeXLMatrixCorrection ✗ ImageSegmentation ✗ Images 210107.8 ms ? NeXLSpectrum Info Given NeXLParticle was explicitly requested, output will be shown live  WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. 70620.9 ms ? NeXLParticle 0 dependencies successfully precompiled in 858 seconds. 399 already precompiled. 4 dependencies failed but may be precompilable after restarting julia 4 dependencies had output during precompilation: ┌ NeXLCore │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLSpectrum │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLMatrixCorrection │ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ NeXLParticle │ [Output was shown above] └ WARNING: Method definition ==(PeriodicTable.Element, PeriodicTable.Element) in module PeriodicTable at /home/pkgeval/.julia/packages/PeriodicTable/S55ll/src/PeriodicTable.jl:279 overwritten in module NeXLCore at /home/pkgeval/.julia/packages/NeXLCore/kYGvK/src/element.jl:56. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. Precompiling packages... 113036.5 ms ✓ TiffImages 7917.0 ms ✓ Compose 16995.5 ms ✓ FLoops ✗ JLD2 7329.3 ms ✓ OpenEXR 4979.6 ms ✓ Interpolations 11577.3 ms ✓ GeometryBasics 2451.2 ms ✓ Rotations → RotationsRecipesBaseExt 3758.6 ms ✓ Polynomials → PolynomialsChainRulesCoreExt 5438.8 ms ✓ OnlineStatsBase 4892.7 ms ✓ TimeZones → TimeZonesRecipesBaseExt 8162.8 ms ✓ ColorSchemes 9373.7 ms ✓ Clustering 15621.0 ms ✓ HDF5 2174.4 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 7237.6 ms ✓ ImageMorphology 8695.6 ms ✓ PNGFiles 16951.7 ms ✓ ImageMagick 15056.1 ms ✓ JpegTurbo 15151.3 ms ✓ Sixel 8360.4 ms ✓ Distributions → DistributionsChainRulesCoreExt 9280.0 ms ✓ ImageAxes 97655.4 ms ✓ ImageFiltering 7134.8 ms ✓ LoopVectorization → ForwardDiffExt 36004.1 ms ✓ NFFT ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1451 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x78e8be8a2f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30242.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3479 [inlined] ijl_apply_generic at /source/src/gf.c:3679 jl_apply at /source/src/julia.h:2348 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30242.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3479 [inlined] ijl_apply_generic at /source/src/gf.c:3679 jl_apply at /source/src/julia.h:2348 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x7cb388459f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30242.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3479 [inlined] ijl_apply_generic at /source/src/gf.c:3679 jl_apply at /source/src/julia.h:2348 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30242.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3479 [inlined] ijl_apply_generic at /source/src/gf.c:3679 jl_apply at /source/src/julia.h:2348 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x00007cb353db0970 Total snapshots: 1. Utilization: 0% ╎1 @Base/task.jl:1150 wait_forever() ╎ 1 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007cb37e3fc100 Total snapshots: 1. Utilization: 0% ╎1 @Base/task.jl:1150 wait_forever() ╎ 1 @Base/task.jl:1216 wait() [1451] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/NeXLParticle/rjtdp/src/NeXLParticle.jl:11 _ZNK4llvm5APInt7compareERKS0_ at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) _ZNK4llvm5APInt8uadd_satERKS0_ at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) _ZN4llvm9KnownBits16computeForAddSubEbbbRKS0_S2_ at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) _ZNK4llvm14TargetLowering20SimplifyDemandedBitsENS_7SDValueERKNS_5APIntES4_RNS_9KnownBitsERNS0_17TargetLoweringOptEjb at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) _ZN12_GLOBAL__N_111DAGCombiner20SimplifyDemandedBitsEN4llvm7SDValueE.constprop.0 at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) _ZN12_GLOBAL__N_111DAGCombiner12visitADDLikeEPN4llvm6SDNodeE at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) PkgEval terminated after 2745.07s: test duration exceeded the time limit