Package evaluation of ReefBiodiversityAccountSetup on Julia 1.13.0-DEV.582 (c0a1728d50*) started at 2025-05-14T22:58:57.799 ################################################################################ # Set-up # Set-up completed after 0.34s ################################################################################ # Installation # Installing ReefBiodiversityAccountSetup... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [0c8e82bf] + ReefBiodiversityAccountSetup v0.1.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.3.0 [35492f91] + AdaptivePredicates v1.2.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 [c9ce4bd3] + ArchGDAL v0.10.8 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.19.0 [67c07d97] + Automa v1.1.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.7 [e1450e63] + BufferedStreams v1.2.2 [fa961155] + CEnum v0.5.0 ⌅ [179af706] + CFTime v0.1.4 [96374032] + CRlibm v1.0.2 [336ed68f] + CSV v0.10.15 [d360d2e6] + ChainRulesCore v1.25.1 [944b1d66] + CodecZlib v0.7.8 [a2cac450] + ColorBrewer v0.4.1 [35d6a980] + ColorSchemes v3.29.0 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌃ [c3611d14] + ColorVectorSpace v0.10.0 [5ae59095] + Colors v0.13.0 [1fbeeb36] + CommonDataModel v0.3.8 [bbf7d656] + 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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 To see why use `status --outdated -m` Installation completed after 12.16s ################################################################################ # Precompilation # Precompiling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... 4853.7 ms ✓ YAXArrayBase → DimensionalDataExt 14201.9 ms ✓ Rasters 9366.3 ms ✓ GeometryOps → GeometryOpsProjExt 102144.0 ms ? GraphMakie 513297.7 ms ✓ DimensionalData → DimensionalDataMakie 43316.5 ms ✓ ArchGDAL → ArchGDALMakieExt 20630.6 ms ✓ GeoDataFrames 9489.6 ms ✓ YAXArrayBase → ArchGDALExt 435002.2 ms ? GLMakie ✗ YAXArrays 103293.5 ms ✓ Rasters → RastersMakieExt 12051.5 ms ✓ Rasters → RastersProjExt 5617.4 ms ✓ Rasters → RastersCoordinateTransformationsExt 20675.8 ms ✓ Rasters → RastersNCDatasetsExt 5462.0 ms ✓ Rasters → RastersStatsBaseExt 47878.6 ms ✓ Rasters → RastersArchGDALExt 425366.7 ms ? GeoMakie 31834.4 ms ? ReefBiodiversityAccountSetup 13 dependencies successfully precompiled in 1833 seconds. 408 already precompiled. 4 dependencies failed but may be precompilable after restarting julia 5 dependencies had output during precompilation: ┌ GLMakie │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Statistics.cov), SparseArrays.SparseMatrixCSC{Tv, Ti} where Ti<:Integer where Tv) in module SparseArraysExt at /home/pkgeval/.julia/packages/Statistics/gbcbG/ext/SparseArraysExt.jl:14 overwritten in module SparseArraysExt 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. └ ┌ GraphMakie │ WARNING: Method definition (::Type{ChainRulesCore.ProjectTo{P, D} where D<:(NamedTuple{names, T} where T<:Tuple where names) where P})(SparseArrays.SparseVector{T, Ti} where Ti<:Integer) where {T<:Number} in module ChainRulesCoreSparseArraysExt at /home/pkgeval/.julia/packages/ChainRulesCore/U6wNx/ext/ChainRulesCoreSparseArraysExt.jl:14 overwritten in module ChainRulesCoreSparseArraysExt 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. └ ┌ GeoMakie │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Statistics.cov), SparseArrays.SparseMatrixCSC{Tv, Ti} where Ti<:Integer where Tv) in module SparseArraysExt at /home/pkgeval/.julia/packages/Statistics/gbcbG/ext/SparseArraysExt.jl:14 overwritten in module SparseArraysExt 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. └ ┌ Rasters → RastersMakieExt │ WARNING: Detected access to binding `Dimensions.X` 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. │ To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`. │ WARNING: Detected access to binding `Dimensions.Y` 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. │ To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`. │ WARNING: Detected access to binding `DimensionalData.DimArray` 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. │ To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`. │ WARNING: Detected access to binding `Dimensions.Z` 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. │ To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`. │ WARNING: Detected access to binding `DimensionalData.DimStack` 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. │ To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`. └ ┌ ReefBiodiversityAccountSetup │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compat.get_num_threads), Any...) in module CompatLinearAlgebraExt at deprecated.jl:223 overwritten in module CompatLinearAlgebraExt 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. └ Precompilation completed after 1836.28s ################################################################################ # Loading # Loading ReefBiodiversityAccountSetup... Precompiling packages... ✗ YAXArrays 9593.0 ms ✓ GeometryOps → GeometryOpsProjExt 447542.9 ms ✓ GraphMakie 60389.4 ms ✓ DimensionalData → DimensionalDataMakie 45802.1 ms ✓ ArchGDAL → ArchGDALMakieExt 9803.7 ms ✓ YAXArrayBase → ArchGDALExt ✗ GLMakie ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 440 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x759ee59a5f14) 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_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [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_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [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 0x0000759ece3b06a0 Total snapshots: 218. Utilization: 0% ╎218 @Base/task.jl:1150 wait_forever() 217╎ 218 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x0000759ecfdfc100 Total snapshots: 218. Utilization: 0% ╎218 @Base/task.jl:1150 wait_forever() 217╎ 218 @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: 0x7d6c77ee6f14) 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_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [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_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [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 0x00007d6c615d1d20 Total snapshots: 229. Utilization: 0% ╎229 @Base/task.jl:1150 wait_forever() 228╎ 229 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007d6c623fc100 Total snapshots: 229. Utilization: 0% ╎229 @Base/task.jl:1150 wait_forever() 228╎ 229 @Base/task.jl:1216 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 unknown function (ip: 0x7d6c77ee6f14) 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 [440] signal 15: Terminated in expression starting at none:1 unknown function (ip: 0x759ee59a5f14) 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 at ./task.jl:1216 wait_forever at ./task.jl:1150 wait_forever at ./task.jl:1150 jfptr_wait_forever_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jfptr_wait_forever_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [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) jl_apply at /source/src/julia.h:2345 [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 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 at ./task.jl:1216 wait_forever at ./task.jl:1150 wait_forever at ./task.jl:1150 jfptr_wait_forever_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 15359209 (Pool: 15358637; Big: 572); GC: 11 jfptr_wait_forever_30607.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 12905581 (Pool: 12905366; Big: 215); GC: 27 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") error at ./error.jl:44 #schedule#595 at ./task.jl:1035 schedule at ./task.jl:1027 [inlined] uv_writecb_task at ./stream.jl:1200 jlcapi_YY.uv_writecb_task_21665.1 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_process_events at /source/src/jl_uv.c:393 process_events at ./libuv.jl:126 [inlined] wait at ./task.jl:1201 uv_write at ./stream.jl:1081 unsafe_write at ./stream.jl:1154 write at ./strings/io.jl:242 [inlined] print at ./strings/io.jl:244 jfptr_print_71633.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 showerror at ./errorshow.jl:161 unknown function (ip: 0x759ee43bd926) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 _atexit at ./initdefs.jl:467 unknown function (ip: 0x759ee43bd894) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2345 [inlined] ijl_atexit_hook at /source/src/init.c:260 jl_exit_thread0_cb at /source/src/signals-unix.c:564 PkgEval terminated after 2758.64s: test duration exceeded the time limit