Package evaluation to test PALEOaqchem on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T14:41:23.414


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.11`

Set-up completed after 7.9s


################################################################################
# Installation
#

Installing PALEOaqchem...
   Resolving package versions...
    Updating `~/.julia/environments/v1.11/Project.toml`
  [673cec3b] + PALEOaqchem v0.3.19
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [79e6a3ab] + Adapt v4.4.0
  [ec485272] + ArnoldiMethod v0.4.0
  [a9b6321e] + Atomix v1.1.2
  [13072b0f] + AxisAlgorithms v1.1.0
  [6e4b80f9] + BenchmarkTools v1.6.3
  [e1450e63] + BufferedStreams v1.2.2
  [179af706] + CFTime v0.2.5
  [d360d2e6] + ChainRulesCore v1.26.0
  [da1fd8a2] + CodeTracking v3.0.0
  [944b1d66] + CodecZlib v0.7.8
  [1fbeeb36] + CommonDataModel v0.4.2
  [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 v1.8.1
  [864edb3b] + DataStructures v0.19.3
  [e2d170a0] + DataValueInterfaces v1.0.0
  [3c3547ce] + DiskArrays v0.4.18
  [ffbed154] + DocStringExtensions v0.9.5
  [e2ba6199] + ExprTools v0.1.10
  [86223c79] + Graphs v1.13.3
  [f67ccb44] + HDF5 v0.17.2
  [5903a43b] + Infiltrator v1.9.7
  [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 v1.7.1
  [682c06a0] + JSON v1.4.0
  [aa1ae85d] + JuliaInterpreter v0.10.9
  [8ac3fa9e] + LRUCache v1.6.2
  [b964fa9f] + LaTeXStrings v1.4.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [6f1432cf] + LoweredCodeUtils v3.5.0
⌅ [23992714] + MAT v0.10.7
  [3da0fdf6] + MPIPreferences v0.1.11
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] + Missings v1.2.0
  [85f8d34a] + NCDatasets v0.14.10
  [6fe1bfb0] + OffsetArrays v1.17.0
  [bac558e1] + OrderedCollections v1.8.1
  [673cec3b] + PALEOaqchem v0.3.19
⌃ [804b410e] + PALEOboxes v0.22.3
  [69de0a69] + Parsers v2.8.3
  [2dfb63ee] + PooledArrays v1.4.3
⌅ [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.5.1
  [08abe8d2] + PrettyTables v3.1.2
  [c84ed2f1] + Ratios v0.4.5
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [295af30f] + Revise v3.13.1
  [fdea26ae] + SIMD v3.7.2
  [91c51154] + SentinelArrays v1.4.9
  [699a6c99] + SimpleTraits v0.9.5
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.6.1
  [90137ffa] + StaticArrays v1.9.16
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [69024149] + StringEncodings v0.3.7
  [892a3eda] + StringManipulation v0.4.2
  [09ab397b] + StructArrays v0.7.2
  [ec057cc2] + StructUtils v2.6.2
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [1e6cf692] + TestEnv v1.103.2
  [a759f4b9] + TimerOutputs v0.5.29
  [3bb67fe8] + TranscodingStreams v0.11.3
  [013be700] + UnsafeAtomics v0.3.0
  [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 v1.14.6+0
  [e33a78d0] + Hwloc_jll v2.12.2+0
  [1d63c593] + LLVMOpenMP_jll v18.1.8+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 v5.0.9+0
  [458c3c95] + OpenSSL_jll v3.5.4+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 v5.8.2+0
  [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0
  [3161d3a3] + Zstd_jll v1.5.7+1
  [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
  [8ba89e20] + Distributed v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.11.0
  [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 v1.11.0
  [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 v1.1.1+0
  [deac9b47] + LibCURL_jll v8.6.0+0
  [e37daf67] + LibGit2_jll v1.7.2+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+0
  [14a3606d] + MozillaCACerts_jll v2023.12.12
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [05823500] + OpenLibm_jll v0.8.5+0
  [bea87d4a] + SuiteSparse_jll v7.7.0+0
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0
  [8e850ede] + nghttp2_jll v1.59.0+0
  [3f19e933] + p7zip_jll v17.4.0+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`

Installation completed after 10.79s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

┌ Warning: Could not use exact versions of packages in manifest, re-resolving
└ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.11/activate_set.jl:78
Precompiling package dependencies...
Precompiling project...
  54242.5 ms  ✓ NonlinearSolveBase → NonlinearSolveBaseSparseMatrixColoringsExt
  34948.8 ms  ✓ SparseDiffTools → SparseDiffToolsPolyesterExt
  76829.3 ms  ✓ BracketingNonlinearSolve → BracketingNonlinearSolveForwardDiffExt
  69677.8 ms  ✓ LineSearch → LineSearchLineSearchesExt
  23769.1 ms  ✓ LinearSolve → LinearSolveSparspakExt
 117457.1 ms  ✓ PALEOboxes
  41417.1 ms  ✓ Sundials
 155910.8 ms  ✓ OrdinaryDiffEqDifferentiation
 122552.9 ms  ✓ NonlinearSolveFirstOrder
  24185.0 ms  ✓ NonlinearSolveSpectralMethods → NonlinearSolveSpectralMethodsForwardDiffExt
  43681.6 ms  ✓ NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
   8549.2 ms  ✓ BracketingNonlinearSolve → BracketingNonlinearSolveChainRulesCoreExt
  39600.0 ms  ✓ SimpleNonlinearSolve
  30423.8 ms  ✓ PALEOaqchem
 198854.3 ms  ✓ PALEOmodel
  85471.4 ms  ✓ OrdinaryDiffEqExponentialRK
  14534.0 ms  ✓ OrdinaryDiffEqExtrapolation
  52132.6 ms  ✓ OrdinaryDiffEqRosenbrock
  36580.1 ms  ✓ SimpleNonlinearSolve → SimpleNonlinearSolveDiffEqBaseExt
   4245.8 ms  ✓ SimpleNonlinearSolve → SimpleNonlinearSolveChainRulesCoreExt
 208087.3 ms  ✓ PALEOocean
 359071.2 ms  ✓ NonlinearSolve
 383505.1 ms  ✓ NonlinearSolve → NonlinearSolveNLsolveExt
 336096.5 ms  ✓ NonlinearSolve → NonlinearSolveSundialsExt
  45200.9 ms  ✓ OrdinaryDiffEqNonlinearSolve
  21811.5 ms  ✓ OrdinaryDiffEqStabilizedIRK
  19340.0 ms  ✓ OrdinaryDiffEqSDIRK

======================================================================================
Information request received. A stacktrace will print followed by a 1.0 second profile
======================================================================================

cmd: /opt/julia/bin/julia 47 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:522
poptask at ./task.jl:1012
wait at ./task.jl:1021
#wait#733 at ./condition.jl:130
wait at ./condition.jl:125 [inlined]
_trywait at ./asyncevent.jl:145
#818 at ./asyncevent.jl:311
jfptr_YY.818_67287.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
start_task at /source/src/task.c:1204
unknown function (ip: (nil))

==============================================================
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/v1.11/Profile/src/Profile.jl:1240
Overhead ╎ [+additional indent] Count File:Line; Function
=========================================================
Thread 1 Task 0x00007b7190eedc30 Total snapshots: 266. Utilization: 0%
   ╎266 @Base/asyncevent.jl:311; (::Base.var"#818#819"{FileWatching.Pidfile.var…
   ╎ 266 @Base/asyncevent.jl:145; _trywait(t::Timer)
   ╎  266 @Base/condition.jl:125; wait
   ╎   266 @Base/condition.jl:130; wait(c::Base.GenericCondition{Base.Threads.S…
   ╎    266 @Base/task.jl:1021; wait()
265╎     266 @Base/task.jl:1012; 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:522
poptask at ./task.jl:1012
wait at ./task.jl:1021
task_done_hook at ./task.jl:694
jfptr_task_done_hook_66687.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
jl_finish_task at /source/src/task.c:315
start_task at /source/src/task.c:1215
unknown function (ip: (nil))

==============================================================
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/v1.11/Profile/src/Profile.jl:1240
Overhead ╎ [+additional indent] Count File:Line; Function
=========================================================
Thread 1 Task 0x000075b13032f3a0 Total snapshots: 328. Utilization: 0%
   ╎328 @Base/task.jl:694; task_done_hook(t::Task)
   ╎ 328 @Base/task.jl:1021; wait()
327╎  328 @Base/task.jl:1012; poptask(W::Base.IntrusiveLinkedListSynchronized{T…


[47] 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:522

[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:522
poptask at ./task.jl:1012
poptask at ./task.jl:1012
wait at ./task.jl:1021
wait at ./task.jl:1021
#wait#733 at ./condition.jl:130
#wait#733 at ./condition.jl:130
wait at ./condition.jl:125 [inlined]
_trywait at ./asyncevent.jl:145
wait at ./condition.jl:125 [inlined]
_trywait at ./asyncevent.jl:145
#818 at ./asyncevent.jl:311
profile_printing_listener at ./Base.jl:582
#1192 at ./Base.jl:622
jfptr_YY.818_67287.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
start_task at /source/src/task.c:1204
unknown function (ip: (nil))
Allocations: 45544632 (Pool: 45541521; Big: 3111); GC: 43
val already in a list
atexit hook threw an error: ErrorException("schedule: Task not runnable")
jfptr_YY.1192_76260.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
start_task at /source/src/task.c:1204
unknown function (ip: (nil))
Allocations: 14917712 (Pool: 14915498; Big: 2214); GC: 15
error at ./error.jl:35
val already in a list
atexit hook threw an error: ErrorException("schedule: Task not runnable")
#schedule#763 at ./task.jl:884
error at ./error.jl:35
schedule at ./task.jl:876 [inlined]
uv_writecb_task at ./stream.jl:1200
#schedule#763 at ./task.jl:884
schedule at ./task.jl:876 [inlined]
uv_writecb_task at ./stream.jl:1200
jfptr_uv_writecb_task_67137.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jfptr_uv_writecb_task_67137.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jlcapi_uv_writecb_task_67601.1 at /opt/julia/lib/julia/sys.so (unknown line)
uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926
uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227
uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824
uv_run at /workspace/srcdir/libuv/src/unix/core.c:420
ijl_task_get_next at /source/src/scheduler.c:522
jlcapi_uv_writecb_task_67601.1 at /opt/julia/lib/julia/sys.so (unknown line)
uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926
uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227
poptask at ./task.jl:1012
uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824
uv_run at /workspace/srcdir/libuv/src/unix/core.c:420
ijl_task_get_next at /source/src/scheduler.c:522
wait at ./task.jl:1021
poptask at ./task.jl:1012
uv_write at ./stream.jl:1081
wait at ./task.jl:1021
unsafe_write at ./stream.jl:1154
uv_write at ./stream.jl:1081
write at ./strings/io.jl:248 [inlined]
print at ./strings/io.jl:250
unsafe_write at ./stream.jl:1154
write at ./strings/io.jl:248 [inlined]
print at ./strings/io.jl:250
jfptr_print_48487.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
showerror at ./errorshow.jl:152
unknown function (ip: 0x7b719c4c8e66)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jfptr_print_48487.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
showerror at ./errorshow.jl:152
unknown function (ip: 0x75b137d58686)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
_atexit at ./initdefs.jl:454
_atexit at ./initdefs.jl:454
jfptr__atexit_69645.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
ijl_atexit_hook at /source/src/init.c:271
jl_exit_thread0_cb at /source/src/signals-unix.c:517
jfptr__atexit_69645.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
ijl_atexit_hook at /source/src/init.c:271
jl_exit_thread0_cb at /source/src/signals-unix.c:517

PkgEval terminated after 2734.72s: test duration exceeded the time limit