Package evaluation to test LeafOptics on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-11T21:44:04.617 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.28s ################################################################################ # Installation # Installing LeafOptics... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [d155caf3] + LeafOptics v0.3.4 Updating `~/.julia/environments/v1.14/Manifest.toml` [179af706] + CFTime v0.2.4 [781d2db2] + ClimaCache v1.1.8 [1fbeeb36] + CommonDataModel v0.4.1 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [3c3547ce] + DiskArrays v0.4.18 [ffbed154] + DocStringExtensions v0.9.5 [f1e47f7f] + EmeraldConstants v0.1.0 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [8ac3fa9e] + LRUCache v1.6.2 [b964fa9f] + LaTeXStrings v1.4.0 [d155caf3] + LeafOptics v0.3.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [e1d29d7a] + Missings v1.2.0 [6a36f34d] + NetcdfIO v0.2.10 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [0d262f2c] + PkgUtility v0.2.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3a884ed6] + UnPack v1.0.2 [0b7ba130] + Blosc_jll v1.21.7+0 [6e34b625] + Bzip2_jll v1.0.9+0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [7243133f] + NetCDF_jll v401.900.300+0 [fe0851c0] + OpenMPI_jll v5.0.8+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [ffd25f8a] + XZ_jll v5.8.1+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+0 [337d8026] + libzip_jll v1.11.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates 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 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [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 v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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 11.18s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 9623.1 ms ✓ StatsBase 10310.8 ms ✓ PkgUtility 19707.5 ms ✓ LeafOptics 3 dependencies successfully precompiled in 41 seconds. 99 already precompiled. Precompilation completed after 57.66s ################################################################################ # Testing # Testing LeafOptics Status `/tmp/jl_ysbmjI/Project.toml` [781d2db2] ClimaCache v1.1.8 [f1e47f7f] EmeraldConstants v0.1.0 [d155caf3] LeafOptics v0.3.4 [276daf66] SpecialFunctions v2.6.1 [3a884ed6] UnPack v1.0.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_ysbmjI/Manifest.toml` [179af706] CFTime v0.2.4 [781d2db2] ClimaCache v1.1.8 [1fbeeb36] CommonDataModel v0.4.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [3c3547ce] DiskArrays v0.4.18 [ffbed154] DocStringExtensions v0.9.5 [f1e47f7f] EmeraldConstants v0.1.0 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [8ac3fa9e] LRUCache v1.6.2 [b964fa9f] LaTeXStrings v1.4.0 [d155caf3] LeafOptics v0.3.4 [2ab3a3ac] LogExpFunctions v0.3.29 [3da0fdf6] MPIPreferences v0.1.11 [e1d29d7a] Missings v1.2.0 [6a36f34d] NetcdfIO v0.2.10 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [0d262f2c] PkgUtility v0.2.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3a884ed6] UnPack v1.0.2 [0b7ba130] Blosc_jll v1.21.7+0 [6e34b625] Bzip2_jll v1.0.9+0 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [5ced341a] Lz4_jll v1.10.1+0 [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [7243133f] NetCDF_jll v401.900.300+0 [fe0851c0] OpenMPI_jll v5.0.8+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [ffd25f8a] XZ_jll v5.8.1+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] libaec_jll v1.1.4+0 [337d8026] libzip_jll v1.11.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates 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 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [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 v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Spectra: Error During Test at /home/pkgeval/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:8 Got exception outside of a @test DomainError with -0.24246158: sqrt was called with a negative real argument but will only return a complex result if called with a complex argument. Try sqrt(Complex(x)). Stacktrace: [1] throw_complex_domainerror(f::Symbol, x::Float32) @ Base.Math ./math.jl:33 [2] sqrt @ ./math.jl:645 [inlined] [3] average_transmittance(α::Float32, nr::Float32) @ LeafOptics ~/.julia/packages/LeafOptics/GJx0S/src/transmittance.jl:41 [4] _broadcast_getindex_evalf @ ./broadcast.jl:698 [inlined] [5] _broadcast_getindex @ ./broadcast.jl:671 [inlined] [6] _getindex @ ./broadcast.jl:619 [inlined] [7] getindex @ ./broadcast.jl:615 [inlined] [8] macro expansion @ ./broadcast.jl:994 [inlined] [9] macro expansion @ ./simdloop.jl:77 [inlined] [10] copyto! @ ./broadcast.jl:993 [inlined] [11] copyto! @ ./broadcast.jl:946 [inlined] [12] copy @ ./broadcast.jl:918 [inlined] [13] materialize @ ./broadcast.jl:893 [inlined] [14] leaf_spectra!(bio::ClimaCache.HyperspectralLeafBiophysics{Float32}, wls::ClimaCache.WaveLengthSet{Float32}, lha::ClimaCache.HyperspectralAbsorption{Float32}, lwc::Float32; APAR_car::Bool, reabsorb::Bool, α::Float32) @ LeafOptics ~/.julia/packages/LeafOptics/GJx0S/src/spectra.jl:106 [15] leaf_spectra!(bio::ClimaCache.HyperspectralLeafBiophysics{Float32}, wls::ClimaCache.WaveLengthSet{Float32}, lha::ClimaCache.HyperspectralAbsorption{Float32}, lwc::Float32) @ LeafOptics ~/.julia/packages/LeafOptics/GJx0S/src/spectra.jl:72 [16] macro expansion @ ~/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:15 [inlined] [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:9 [inlined] [19] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [20] top-level scope @ ~/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:8 [21] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [22] top-level scope @ none:6 [23] eval(m::Module, e::Any) @ Core ./boot.jl:489 [24] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [25] _start() @ Base ./client.jl:577 SIF: Error During Test at /home/pkgeval/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:45 Got exception outside of a @test DimensionMismatch: incompatible dimensions for matrix multiplication: tried to multiply a matrix of size (29, 45) with a vector of length 0. The second dimension of the matrix: 45, does not match the length of the vector: 0. Stacktrace: [1] matmul_size_check_error(sizeA::Tuple{Int64, Int64}, sizeB::Tuple{Int64}) @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:436 [2] matmul_size_check @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:423 [inlined] [3] matmul_size_check @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:446 [inlined] [4] gemv! @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:697 [inlined] [5] generic_matvecmul! @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:81 [inlined] [6] _mul! @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:76 [inlined] [7] mul! @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:73 [inlined] [8] _mat_vec_scalar @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:1400 [inlined] [9] mat_vec_scalar @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:1394 [inlined] [10] * @ /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/matmul.jl:1364 [inlined] [11] leaf_SIF(bio::ClimaCache.HyperspectralLeafBiophysics{Float32}, wls::ClimaCache.WaveLengthSet{Float32}, rad::ClimaCache.HyperspectralRadiation{Float32}, ϕ::Float32; ϕ_photon::Bool) @ LeafOptics ~/.julia/packages/LeafOptics/GJx0S/src/fluorescence.jl:53 [12] leaf_SIF(bio::ClimaCache.HyperspectralLeafBiophysics{Float32}, wls::ClimaCache.WaveLengthSet{Float32}, rad::ClimaCache.HyperspectralRadiation{Float32}, ϕ::Float32) @ LeafOptics ~/.julia/packages/LeafOptics/GJx0S/src/fluorescence.jl:35 [13] macro expansion @ ~/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:51 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [15] macro expansion @ ~/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:46 [inlined] [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [17] top-level scope @ ~/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:8 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [22] _start() @ Base ./client.jl:577 Test Summary: | Pass Error Total Time LeafOptics CI Coverage | 12 2 14 4m57.5s Spectra | 1 1 4m45.0s PAR & APAR | 4 4 7.4s SIF | 1 1 1.5s Utils | 8 8 3.5s RNG of the outermost testset: Random.Xoshiro(0x349f099fee6f8e66, 0xc631b828e97c03d3, 0x8a9b9c26cdecc982, 0x269ea17639765bed, 0x4a94a91842c00ce4) ERROR: LoadError: Some tests did not pass: 12 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/LeafOptics/GJx0S/test/runtests.jl:6 Testing failed after 336.96s ERROR: LoadError: Package LeafOptics errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 441.89s: package tests unexpectedly errored