Package evaluation of PlantBiophysics on Julia 1.13.0-DEV.985 (9c94e7ae32*) started at 2025-08-15T02:23:58.164 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.73s ################################################################################ # Installation # Installing PlantBiophysics... Resolving package versions... Installed DefineSingletons ──────────── v0.1.2 Installed LsqFit ────────────────────── v0.15.1 Installed OrderedCollections ────────── v1.8.1 Installed InlineStrings ─────────────── v1.4.4 Installed InitialValues ─────────────── v0.3.1 Installed ContextVariablesX ─────────── v0.1.3 Installed FLoops ────────────────────── v0.2.2 Installed ArgCheck ──────────────────── v2.5.0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed SentinelArrays ────────────── v1.4.8 Installed NaNMath ───────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed ScopedValues ──────────────── v1.4.0 Installed FileIO ────────────────────── v1.17.0 Installed Tables ────────────────────── v1.12.1 Installed Reexport ──────────────────── v1.2.2 Installed InverseFunctions ──────────── v0.1.17 Installed NLSolversBase ─────────────── v7.10.0 Installed Missings ──────────────────── v1.2.0 Installed FLoopsBase ────────────────── v0.1.1 Installed Preferences ───────────────── v1.5.0 Installed UnPack ────────────────────── v1.0.2 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed TableTraits ───────────────── v1.0.1 Installed MultiScaleTreeGraph ───────── v0.14.4 Installed ADTypes ───────────────────── v1.17.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed Inflate ───────────────────── v0.1.5 Installed DiffResults ───────────────── v1.1.0 Installed MacroTools ────────────────── v0.5.16 Installed MLStyle ───────────────────── v0.4.17 Installed URIs ──────────────────────── v1.6.1 Installed FillArrays ────────────────── v1.13.0 Installed DataStructures ────────────── v0.18.22 Installed UnicodeFun ────────────────── v0.4.1 Installed CodecZlib ─────────────────── v0.7.8 Installed AbstractTrees ─────────────── v0.4.5 Installed ArnoldiMethod ─────────────── v0.4.0 Installed ArrayInterface ────────────── v7.19.0 Installed StatsBase ─────────────────── v0.34.6 Installed DelimitedFiles ────────────── v1.9.1 Installed DataValueInterfaces ───────── v1.0.0 Installed MutableNamedTuples ────────── v0.1.3 Installed CommonSubexpressions ──────── v0.3.1 Installed IrrationalConstants ───────── v0.2.4 Installed LoggingExtras ─────────────── v1.1.0 Installed ZipArchives ───────────────── v2.5.1 Installed PrettyPrint ───────────────── v0.2.0 Installed HTTP ──────────────────────── v1.10.17 Installed SimpleTraits ──────────────── v0.9.5 Installed BitFlags ──────────────────── v0.1.9 Installed SplittablesBase ───────────── v0.1.15 Installed SimpleBufferStream ────────── v1.2.0 Installed Setfield ──────────────────── v1.1.2 Installed Baselet ───────────────────── v0.1.1 Installed PooledArrays ──────────────── v1.4.3 Installed PDMats ────────────────────── v0.11.35 Installed Transducers ───────────────── v0.4.84 Installed WorkerUtilities ───────────── v1.6.1 Installed DocStringExtensions ───────── v0.9.5 Installed CompositionsBase ──────────── v0.1.2 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed MyterialColors ────────────── v0.3.0 Installed ForwardDiff ───────────────── v1.0.1 Installed NameResolution ────────────── v0.1.5 Installed AliasTables ───────────────── v1.1.3 Installed PlantBiophysics ───────────── v0.16.2 Installed DifferentiationInterface ──── v0.7.4 Installed ConcurrentUtilities ───────── v2.5.0 Installed RecipesBase ───────────────── v1.3.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed HashArrayMappedTries ──────── v0.2.0 Installed ZipFile ───────────────────── v0.10.1 Installed InvertedIndices ───────────── v1.3.1 Installed DataAPI ───────────────────── v1.16.0 Installed MetaGraphsNext ────────────── v0.7.3 Installed CodecInflate64 ────────────── v0.1.3 Installed StaticArraysCore ──────────── v1.4.3 Installed CodeTracking ──────────────── v1.3.9 Installed BangBang ──────────────────── v0.4.4 Installed StringManipulation ────────── v0.4.1 Installed StaticArrays ──────────────── v1.9.14 Installed Requires ──────────────────── v1.3.1 Installed PlantSimEngine ────────────── v0.13.2 Installed LogExpFunctions ───────────── v0.3.29 Installed DiffRules ─────────────────── v1.15.1 Installed Term ──────────────────────── v2.0.7 Installed JSON ──────────────────────── v0.21.4 Installed PrettyTables ──────────────── v2.4.0 Installed Parsers ───────────────────── v2.8.3 Installed FiniteDiff ────────────────── v2.28.0 Installed Distributions ─────────────── v0.25.120 Installed Rmath ─────────────────────── v0.8.0 Installed StatsFuns ─────────────────── v1.5.0 Installed WeakRefStrings ────────────── v1.4.2 Installed JLLWrappers ───────────────── v1.7.1 Installed EzXML ─────────────────────── v1.2.2 Installed CSV ───────────────────────── v0.10.15 Installed DataFrames ────────────────── v1.7.0 Installed Accessors ─────────────────── v0.1.42 Installed XLSX ──────────────────────── v0.10.4 Installed MicroCollections ──────────── v0.2.0 Installed PlantMeteo ────────────────── v0.6.1 Installed FilePathsBase ─────────────── v0.9.24 Installed Graphs ────────────────────── v1.13.0 Installed Adapt ─────────────────────── v4.3.0 Installed ConstructionBase ──────────── v1.6.0 Installed HypergeometricFunctions ───── v0.3.28 Installed ExceptionUnwrapping ───────── v0.1.11 Installed TranscodingStreams ────────── v0.11.3 Installed JLD2 ──────────────────────── v0.5.15 Installed JuliaVariables ────────────── v0.2.4 Installed Compat ────────────────────── v4.18.0 Installed ProgressLogging ───────────── v0.1.5 Installed Statistics ────────────────── v1.11.1 Installed StatsAPI ──────────────────── v1.7.1 Installed StringEncodings ───────────── v0.3.7 Installed OpenSSL ───────────────────── v1.5.0 Installed MbedTLS ───────────────────── v1.1.9 Installed PrecompileTools ───────────── v1.3.2 Installed XML2_jll ──────────────────── v2.14.4+0 Installed PtrArrays ─────────────────── v1.3.0 Installed YAML ──────────────────────── v0.4.14 Installed Parameters ────────────────── v0.12.3 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed MbedTLS_jll ───────────────── v2.28.6+2 Installed SpecialFunctions ──────────── v2.5.1 Installed Highlights ────────────────── v0.5.3 Installed InputBuffers ──────────────── v1.1.1 Installing 6 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact XLSX_relocatable_data 6.0 KiB Installed artifact Libiconv 1.9 MiB Installed artifact MbedTLS 2.1 MiB Installed artifact XML2 2.5 MiB Updating `~/.julia/environments/v1.13/Project.toml` [7ae8fcfa] + PlantBiophysics v0.16.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.17.0 [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 v7.19.0 [198e06fe] + BangBang v0.4.4 [9718e550] + Baselet v0.1.1 [d1d4a3ce] + BitFlags v0.1.9 [336ed68f] + CSV v0.10.15 ⌅ [da1fd8a2] + CodeTracking v1.3.9 [6309b1aa] + CodecInflate64 v0.1.3 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.0 [a33af91c] + CompositionsBase v0.1.2 [f0e56b4a] + ConcurrentUtilities v2.5.0 [187b0558] + ConstructionBase v1.6.0 [6add18c4] + ContextVariablesX v0.1.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.4 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [8f5d6c58] + EzXML v1.2.2 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.28.0 [f6369f11] + ForwardDiff v1.0.1 [86223c79] + Graphs v1.13.0 [cd3eb016] + HTTP v1.10.17 [076d061b] + HashArrayMappedTries v0.2.0 [eafb193a] + Highlights v0.5.3 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [22cec73e] + InitialValues v0.3.1 [842dd82b] + InlineStrings v1.4.4 [0c81fc1b] + InputBuffers v1.1.1 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v0.21.4 [b14d175d] + JuliaVariables v0.2.4 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.1.0 [2fda8390] + LsqFit v0.15.1 [d8e11817] + MLStyle v0.4.17 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.9 [fa8bd995] + MetaGraphsNext v0.7.3 [128add7d] + MicroCollections v0.2.0 [e1d29d7a] + Missings v1.2.0 [dd4a991b] + MultiScaleTreeGraph v0.14.4 [af6c499f] + MutableNamedTuples v0.1.3 [1c23619d] + MyterialColors v0.3.0 [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [71a1bf82] + NameResolution v0.1.5 [4d8831e6] + OpenSSL v1.5.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [7ae8fcfa] + PlantBiophysics v0.16.2 [4630fe09] + PlantMeteo v0.6.1 [9a576370] + PlantSimEngine v0.13.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.5.0 [8162dcfd] + PrettyPrint v0.2.0 [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.5 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [7e506255] + ScopedValues v1.4.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [171d559e] + SplittablesBase v0.1.15 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [22787eb5] + Term v2.0.7 [3bb67fe8] + TranscodingStreams v0.11.3 [28d57a85] + Transducers v0.4.84 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [fdbf4ff8] + XLSX v0.10.4 [ddb6d928] + YAML v0.4.14 [49080126] + ZipArchives v2.5.1 [a5390f91] + ZipFile v0.10.1 [94ce4f54] + Libiconv_jll v1.18.0+0 [c8ffd9c3] + MbedTLS_jll v2.28.6+2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [02c8fc9c] + XML2_jll v2.14.4+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 11.76s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4524.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 145 running 0 of 1 signal (10): User defined signal 1 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:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_73644.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2376 [inlined] start_task at /source/src/task.c:1253 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 (default) Task 0x0000703cfc311c30 Total snapshots: 491. Utilization: 0% ╎491 @Base/task.jl:1129 wait_forever() 490╎ 491 @Base/task.jl:1192 wait() ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 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:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_73644.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2376 [inlined] start_task at /source/src/task.c:1253 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 (default) Task 0x000078bd9f5f0c40 Total snapshots: 449. Utilization: 0% ╎449 @Base/task.jl:1129 wait_forever() 448╎ 449 @Base/task.jl:1192 wait() [145] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:37 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:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_73644.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2376 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 19584957 (Pool: 19583214; Big: 1743); GC: 69 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:152 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:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_73644.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2376 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 15470066 (Pool: 15469378; Big: 688); GC: 18 PkgEval terminated after 2736.02s: test duration exceeded the time limit