Package evaluation to test PALEOaqchem on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-20T03:34:25.820 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 7.77s ################################################################################ # Installation # Installing PALEOaqchem... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [673cec3b] + PALEOaqchem v0.3.19 Updating `~/.julia/environments/v1.12/Manifest.toml` [79e6a3ab] + Adapt v4.6.1 [ec485272] + ArnoldiMethod v0.4.0 [a9b6321e] + Atomix v1.1.3 [13072b0f] + AxisAlgorithms v1.1.0 [6e4b80f9] + BenchmarkTools v1.8.0 [e1450e63] + BufferedStreams v1.2.2 [179af706] + CFTime v0.2.10 [d360d2e6] + ChainRulesCore v1.26.1 [da1fd8a2] + CodeTracking v3.0.2 [944b1d66] + CodecZlib v0.7.8 [1fbeeb36] + CommonDataModel v0.4.3 [34da2185] + Compat v4.18.1 [807dbc54] + Compiler v0.1.1 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [3c3547ce] + DiskArrays v0.4.21 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [86223c79] + Graphs v1.14.0 [f67ccb44] + HDF5 v0.17.3 [5903a43b] + Infiltrator v1.9.11 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 ⌅ [a98d9a8b] + Interpolations v0.15.1 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.6.1 [aa1ae85d] + JuliaInterpreter v0.10.12 [8ac3fa9e] + LRUCache v1.6.2 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [6f1432cf] + LoweredCodeUtils v3.6.0 ⌅ [23992714] + MAT v0.10.7 [3da0fdf6] + MPIPreferences v0.1.12 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [85f8d34a] + NCDatasets v0.14.15 [6fe1bfb0] + OffsetArrays v1.17.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [673cec3b] + PALEOaqchem v0.3.19 ⌃ [804b410e] + PALEOboxes v0.22.3 [69de0a69] + Parsers v2.8.6 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [295af30f] + Revise v3.15.1 [fdea26ae] + SIMD v3.7.2 [91c51154] + SentinelArrays v1.4.10 [699a6c99] + SimpleTraits v0.9.6 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.4 [09ab397b] + StructArrays v0.7.3 [ec057cc2] + StructUtils v2.8.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [1e6cf692] + TestEnv v1.103.6 [a759f4b9] + TimerOutputs v0.5.29 [3bb67fe8] + TranscodingStreams v0.11.3 [013be700] + UnsafeAtomics v0.3.1 [efce3f68] + WoodburyMatrices v1.1.0 [ddb6d928] + YAML v0.4.16 [0b7ba130] + Blosc_jll v1.21.7+0 [6e34b625] + Bzip2_jll v1.0.9+0 [0234f1f7] + HDF5_jll v2.1.2+0 [e33a78d0] + Hwloc_jll v2.14.0+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [b5ada748] + MPIABI_jll v0.1.5+0 [7cb0a576] + MPICH_jll v5.0.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.6+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [7243133f] + NetCDF_jll v401.1000.0+0 [fe0851c0] + OpenMPI_jll v5.0.11+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [63e82ce6] + SLEEF_jll v3.9.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [ffd25f8a] + XZ_jll v5.8.3+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.19.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 ⌅ [2b3700d1] + aws_c_auth_jll v0.9.6+0 [70f11efc] + aws_c_cal_jll v0.9.13+0 [73048d1d] + aws_c_common_jll v0.12.6+0 [73a04cd5] + aws_c_compression_jll v0.3.2+0 [3254fc65] + aws_c_http_jll v0.10.13+0 [13c41daa] + aws_c_io_jll v0.26.3+0 ⌅ [bd1f34fb] + aws_c_s3_jll v0.11.5+0 [1282aa60] + aws_c_sdkutils_jll v0.2.4+1 [b2a88e68] + aws_checksums_jll v0.2.10+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [477f73a3] + libaec_jll v1.1.7+0 [337d8026] + libzip_jll v1.11.3+0 [9aeb927a] + mpif_jll v0.1.7+0 [cddc5d3d] + s2n_tls_jll v1.7.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [8bf52ea8] + CRC32c 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 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 v1.12.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+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 v3.5.6+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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` Installation completed after 13.48s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/RUPmD/src/julia-1.12/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 5908.4 ms ✓ SparsityTracing 94976.4 ms ✓ NonlinearSolveBase → NonlinearSolveBaseForwardDiffExt 29758.9 ms ✓ SparseDiffTools → SparseDiffToolsPolyesterExt 12094.4 ms ✓ LinearSolve → LinearSolveForwardDiffExt 104396.6 ms ✓ BracketingNonlinearSolve → BracketingNonlinearSolveForwardDiffExt 93423.2 ms ✓ LineSearch → LineSearchLineSearchesExt 27383.8 ms ✓ LinearSolve → LinearSolveSparspakExt 11580.9 ms ✓ DiffEqBase → DiffEqBaseForwardDiffExt 59350.0 ms ✓ Sundials ✗ PALEOboxes 136930.7 ms ✓ NonlinearSolveSpectralMethods → NonlinearSolveSpectralMethodsForwardDiffExt 126302.3 ms ✓ NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt 12305.7 ms ✓ BracketingNonlinearSolve → BracketingNonlinearSolveChainRulesCoreExt 47036.2 ms ✓ SimpleNonlinearSolve 87554.0 ms ✓ NonlinearSolveFirstOrder 20622.0 ms ✓ OrdinaryDiffEqDifferentiation ✗ PALEOaqchem ✗ PALEOmodel 7079.2 ms ✓ SimpleNonlinearSolve → SimpleNonlinearSolveDiffEqBaseExt 52855.0 ms ✓ SimpleNonlinearSolve → SimpleNonlinearSolveChainRulesCoreExt 94246.2 ms ✓ OrdinaryDiffEqExponentialRK 20807.8 ms ✓ OrdinaryDiffEqExtrapolation 56003.9 ms ✓ OrdinaryDiffEqRosenbrock ✗ PALEOocean 231965.0 ms ✓ NonlinearSolve 534924.1 ms ✓ NonlinearSolve → NonlinearSolveNLsolveExt 500323.1 ms ✓ NonlinearSolve → NonlinearSolveSundialsExt 58562.3 ms ✓ OrdinaryDiffEqNonlinearSolve 29118.5 ms ✓ OrdinaryDiffEqStabilizedIRK 22387.0 ms ✓ OrdinaryDiffEqSDIRK ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 63 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 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #653 at ./asyncevent.jl:359 jfptr_YY.653_3180.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007fdb55ac45b0 Total snapshots: 352. Utilization: 0% ╎352 @Base/asyncevent.jl:359 (::Base.var"#653#654"{FileWatching.Pidfile.var… ╎ 352 @Base/asyncevent.jl:185 _trywait(t::Timer) ╎ 352 @Base/condition.jl:136 wait ╎ 352 @Base/condition.jl:141 wait(c::Base.GenericCondition{Base.Threads.S… ╎ 352 @Base/task.jl:1228 wait() 351╎ 352 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronize… ====================================================================================== 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 poptask at ./task.jl:1216 wait at ./task.jl:1228 task_done_hook at ./task.jl:868 jfptr_task_done_hook_43684.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_finish_task at /source/src/task.c:342 start_task at /source/src/task.c:1264 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/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000722cb50d12d0 Total snapshots: 407. Utilization: 0% ╎407 @Base/task.jl:868 task_done_hook(t::Task) ╎ 407 @Base/task.jl:1228 wait() 406╎ 407 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronized{T… 71691.2 ms ✓ OrdinaryDiffEqFIRK [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:156 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 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 profile_printing_listener at ./Base.jl:332 #start_profile_listener##0 at ./Base.jl:352 jfptr_YY.start_profile_listenerYY.YY.0_10036.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 15555205 (Pool: 15554510; Big: 695); GC: 12 [63] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:34 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 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] wait at ./process.jl:693 wait at ./process.jl:686 [inlined] success at ./process.jl:555 jfptr_success_6905.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #compilecache#914 at ./loading.jl:3236 compilecache at ./loading.jl:3192 [inlined] #_precompilepkgs##36 at ./precompilation.jl:1075 with_logstate at ./logging/logging.jl:542 with_logger at ./logging/logging.jl:653 [inlined] #_precompilepkgs##34 at ./precompilation.jl:1069 [inlined] #mkpidlock#8 at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96 jfptr_YY.mkpidlockYY.8_49511.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 mkpidlock at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93 #mkpidlock#7 at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined] mkpidlock at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 jfptr_mkpidlock_68876.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_f__apply_iterate at /source/src/builtins.c:868 #trymkpidlock#13 at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_f__apply_iterate at /source/src/builtins.c:868 trymkpidlock at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:115 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_f_invoke_in_world at /source/src/builtins.c:900 #invokelatest_gr#239 at ./reflection.jl:1297 [inlined] invokelatest_gr at ./reflection.jl:1289 [inlined] precompile_pkgs_maybe_cachefile_lock at ./precompilation.jl:1310 macro expansion at ./timing.jl:461 [inlined] #_precompilepkgs##30 at ./precompilation.jl:1068 jfptr_YY._precompilepkgsYY.YY.30_3976.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 45612122 (Pool: 45610921; Big: 1201); GC: 36 error in running finalizer: ErrorException("task switch not allowed from inside gc finalizer") ijl_error at /source/src/rtutils.c:43 ijl_switch at /source/src/task.c:677 try_yieldto at ./task.jl:1143 wait at ./task.jl:1229 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] close at ./asyncevent.jl:223 close at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:353 jfptr_close_26663.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 run_finalizer at /source/src/gc-common.c:180 jl_gc_run_finalizers_in_list at /source/src/gc-common.c:270 run_finalizers at /source/src/gc-common.c:316 ijl_gc_collect at /source/src/gc-stock.c:3502 gc at ./gcutils.jl:133 [inlined] temp_cleanup_purge_all at ./file.jl:682 temp_cleanup_atexit at ./file.jl:714 jfptr_temp_cleanup_atexit_47154.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _atexit at ./initdefs.jl:464 jfptr__atexit_34583.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] ijl_atexit_hook at /source/src/init.c:260 jl_exit_thread0_cb at /source/src/signals-unix.c:564 PkgEval terminated after 2739.55s: test duration exceeded the time limit