Package evaluation of SurfaceWaterIntegratedModeling on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T14:10:46.940 ################################################################################ # Set-up # Set-up completed after 0.27s ################################################################################ # Installation # Installing SurfaceWaterIntegratedModeling... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [71e2a337] + SurfaceWaterIntegratedModeling v1.0.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [35492f91] + AdaptivePredicates v1.2.0 [66dad0bd] + AliasTables v1.1.3 [a95523ee] + AlmostBlockDiagonals v0.1.10 [27a7e980] + Animations v0.4.2 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.18.0 [4c555306] + ArrayLayouts v1.11.1 [67c07d97] + Automa v1.1.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.7 [aae01518] + BandedMatrices v1.9.4 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [764a87c0] + BoundaryValueDiffEq v5.16.0 [7227322d] + BoundaryValueDiffEqAscher v1.5.0 [56b672f2] + BoundaryValueDiffEqCore v1.8.0 [85d9eb09] + BoundaryValueDiffEqFIRK v1.6.0 [1a22d4ce] + BoundaryValueDiffEqMIRK v1.6.0 [9255f1d6] + BoundaryValueDiffEqMIRKN 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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 To see why use `status --outdated -m` Installation completed after 10.01s ################################################################################ # Precompilation # Precompiling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... 218701.8 ms ✓ ImageSegmentation 511848.4 ms ✓ SciMLBase → SciMLBaseMakieExt ✗ GLMakie 345199.1 ms ✓ Images 40377.0 ms ? SurfaceWaterIntegratedModeling 3 dependencies successfully precompiled in 1223 seconds. 562 already precompiled. 1 dependencies failed but may be precompilable after restarting julia 3 dependencies had output during precompilation: ┌ SurfaceWaterIntegratedModeling │ WARNING: Method definition setindex(GPUArraysCore.AbstractGPUArray{T, N} where N where T, Any, Int64) in module ArrayInterfaceGPUArraysCoreExt at /home/pkgeval/.julia/packages/ArrayInterface/9wQIY/ext/ArrayInterfaceGPUArraysCoreExt.jl:12 overwritten in module ArrayInterfaceGPUArraysCoreExt 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. └ ┌ ImageSegmentation │ WARNING: Constructor for type "Alg" was extended in `ImageFiltering` without explicit qualification or import. │ NOTE: Assumed "Alg" refers to `Algorithm.Alg`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Alg end`. │ Hint: To silence the warning, qualify `Alg` as `Algorithm.Alg` in the method signature or explicitly `import Algorithm: Alg`. └ ┌ Images │ WARNING: Constructor for type "Alg" was extended in `ImageFiltering` without explicit qualification or import. │ NOTE: Assumed "Alg" refers to `Algorithm.Alg`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Alg end`. │ Hint: To silence the warning, qualify `Alg` as `Algorithm.Alg` in the method signature or explicitly `import Algorithm: Alg`. └ Precompilation completed after 1224.13s ################################################################################ # Loading # Loading SurfaceWaterIntegratedModeling... Precompiling packages... ✗ GLMakie Info Given SurfaceWaterIntegratedModeling was explicitly requested, output will be shown live  WARNING: Detected access to binding `SimpleNonlinearSolve.SimpleNewtonRaphson` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `NonlinearSolveFirstOrder.GeneralizedFirstOrderAlgorithm` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.RadauIIa5` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.LobattoIIIa5` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.LobattoIIIb5` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.LobattoIIIc5` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqMIRK.MIRK2` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqMIRK.MIRK4` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. WARNING: Detected access to binding `BoundaryValueDiffEqMIRK.MIRK6` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding.  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ======================================================================================  cmd: /opt/julia/bin/julia 530 running 1 of 1  signal (10): User defined signal 1 _ZN4llvm11ValueMapperD1Ev at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) _ZN4llvm17CloneFunctionIntoEPNS_8FunctionEPKS0_RNS_8ValueMapIPKNS_5ValueENS_14WeakTrackingVHENS_14ValueMapConfigIS7_NS_3sys10SmartMutexILb0EEEEEEENS_23CloneFunctionChangeTypeERNS_15SmallVectorImplIPNS_10ReturnInstEEEPKcPNS_14ClonedCodeInfoEPNS_20ValueMapTypeRemapperEPNS_17ValueMaterializerE at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) removeAddrspaces at /source/src/llvm-remove-addrspaces.cpp:352 run at /source/src/llvm-remove-addrspaces.cpp:424 run at /source/src/llvm-remove-addrspaces.cpp:450 run at /source/usr/include/llvm/IR/PassManagerInternal.h:90 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.19.1jl (unknown line) run at /source/src/pipeline.cpp:789 operator() at /source/src/jitlayers.cpp:1454 withModuleDo<(anonymous namespace)::sizedOptimizerT::operator()(llvm::orc::ThreadSafeModule) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1415 [inlined] operator() at /source/src/jitlayers.cpp:1567 [inlined] addModule at /source/src/jitlayers.cpp:2026 jl_compile_codeinst_now at /source/src/jitlayers.cpp:630 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:819 jl_compile_method_internal at /source/src/gf.c:2994 _jl_invoke at /source/src/gf.c:3471 [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 494 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: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 ==============================================================  ┌ Error: Profile printing listener crashed │ exception = │ This interactive function requires a stdlib to be loaded, and package code should instead use it directly from that stdlib. │ Stacktrace: │ [1] error(s::String) │ @ Base ./error.jl:44 │ [2] require_stdlib(package_uuidkey::Base.PkgId, ext::Nothing) │ @ Base ./loading.jl:2759 │ [3] require_stdlib │ @ ./loading.jl:2757 [inlined] │ [4] macro expansion │ @ ./some.jl:158 [inlined] │ [5] profile_printing_listener(cond::Base.AsyncCondition) │ @ Base ./Base.jl:330 │ [6] (::Base.var"#start_profile_listener##0#start_profile_listener##1"{Base.AsyncCondition})() │ @ Base ./Base.jl:349 └ @ Base Base.jl:340 ┌ Error: Profile printing listener crashed │ exception = │ This interactive function requires a stdlib to be loaded, and package code should instead use it directly from that stdlib. │ Stacktrace: │ [1] error(s::String) │ @ Base ./error.jl:44 │ [2] require_stdlib(package_uuidkey::Base.PkgId, ext::Nothing) │ @ Base ./loading.jl:2759 │ [3] require_stdlib │ @ ./loading.jl:2757 [inlined] │ [4] macro expansion │ @ ./some.jl:158 [inlined] │ [5] profile_printing_listener(cond::Base.AsyncCondition) │ @ Base ./Base.jl:330 │ [6] (::Base.var"#start_profile_listener##0#start_profile_listener##1"{Base.AsyncCondition})() │ @ Base ./Base.jl:349 └ @ Base Base.jl:340  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ======================================================================================  cmd: /opt/julia/bin/julia 206 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: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 ==============================================================  ┌ Error: Profile printing listener crashed │ exception = │ This interactive function requires a stdlib to be loaded, and package code should instead use it directly from that stdlib. │ Stacktrace: │ [1] error(s::String) │ @ Base ./error.jl:44 │ [2] require_stdlib(package_uuidkey::Base.PkgId, ext::Nothing) │ @ Base ./loading.jl:2759 │ [3] require_stdlib │ @ ./loading.jl:2757 [inlined] │ [4] macro expansion │ @ ./some.jl:158 [inlined] │ [5] profile_printing_listener(cond::Base.AsyncCondition) │ @ Base ./Base.jl:330 │ [6] (::Base.var"#start_profile_listener##0#start_profile_listener##1"{Base.AsyncCondition})() │ @ Base ./Base.jl:349 └ @ Base Base.jl:340  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ======================================================================================  cmd: /opt/julia/bin/julia 202 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: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 ==============================================================  ┌ Error: Profile printing listener crashed │ exception = │ This interactive function requires a stdlib to be loaded, and package code should instead use it directly from that stdlib. │ Stacktrace: │ [1] error(s::String) │ @ Base ./error.jl:44 │ [2] require_stdlib(package_uuidkey::Base.PkgId, ext::Nothing) │ @ Base ./loading.jl:2759 │ [3] require_stdlib │ @ ./loading.jl:2757 [inlined] │ [4] macro expansion │ @ ./some.jl:158 [inlined] │ [5] profile_printing_listener(cond::Base.AsyncCondition) │ @ Base ./Base.jl:330 │ [6] (::Base.var"#start_profile_listener##0#start_profile_listener##1"{Base.AsyncCondition})() │ @ Base ./Base.jl:349 └ @ Base Base.jl:340 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 193 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x723128b0bf14) 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 0x000072311e08e590 Total snapshots: 492. Utilization: 0% ╎492 @Base/task.jl:1150 wait_forever() 491╎ 492 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x000072311e9fc100 Total snapshots: 492. Utilization: 0% ╎492 @Base/task.jl:1150 wait_forever() 491╎ 492 @Base/task.jl:1216 wait() ====================================================================================== 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: 0x7817aabcdf14) 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 0x0000781777dc0970 Total snapshots: 490. Utilization: 0% ╎490 @Base/task.jl:1150 wait_forever() 489╎ 490 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007817a09fc100 Total snapshots: 490. Utilization: 0% ╎490 @Base/task.jl:1150 wait_forever() 489╎ 490 @Base/task.jl:1216 wait()  [202] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/SurfaceWaterIntegratedModeling/OhGXs/src/fill_sequence/fill_sequence.jl:2 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 [193] signal 15: Terminated in expression starting at none:1 unknown function (ip: 0x723128b0bf14) 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 PkgEval terminated after 2762.78s: test duration exceeded the time limit