Package evaluation to load SeuratRDS on Julia 1.14.0-DEV.2373 (cf67ecc88f*) started at 2026-06-13T20:57:40.249 ################################################################################ # Set-up # Set-up completed after 0.13s ################################################################################ # Installation # Installing SeuratRDS... Resolving package versions... Installed VersionParsing ────────────── v1.3.0 Installed DelimitedFiles ────────────── v1.9.1 Installed StatsModels ───────────────── v0.7.10 Installed RCall ─────────────────────── v0.13.18 Installed ShiftedArrays ─────────────── v2.0.0 Installed AliasTables ───────────────── v1.1.3 Installed OrderedCollections ────────── v1.8.2 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed DataStructures ────────────── v0.18.22 Installed StatsBase ─────────────────── v0.34.11 Installed InlineStrings ─────────────── v1.4.5 Installed HypergeometricFunctions ───── v0.3.28 Installed DataAPI ───────────────────── v1.16.0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed InvertedIndices ───────────── v1.3.1 Installed Statistics ────────────────── v1.11.1 Installed DataValueInterfaces ───────── v1.0.0 Installed StatsAPI ──────────────────── v1.8.0 Installed SentinelArrays ────────────── v1.4.10 Installed WinReg ────────────────────── v1.0.0 Installed StructUtils ───────────────── v2.8.2 Installed Compat ────────────────────── v4.18.1 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed IrrationalConstants ───────── v0.2.6 Installed LogExpFunctions ───────────── v1.0.1 Installed PrecompileTools ───────────── v1.3.4 Installed Conda ─────────────────────── v1.10.3 Installed StringManipulation ────────── v0.4.4 Installed Requires ──────────────────── v1.3.1 Installed Parsers ───────────────────── v2.8.5 Installed JSON ──────────────────────── v1.6.1 Installed StatsFuns ─────────────────── v2.1.0 Installed Tables ────────────────────── v1.12.1 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed SpecialFunctions ──────────── v2.8.0 Installed Rmath ─────────────────────── v0.9.0 Installed PtrArrays ─────────────────── v1.4.0 Installed PooledArrays ──────────────── v1.4.3 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed JLLWrappers ───────────────── v1.8.0 Installed DataFrames ────────────────── v1.8.2 Installed SortingAlgorithms ─────────── v1.2.2 Installed Preferences ───────────────── v1.5.2 Installed Crayons ───────────────────── v4.1.1 Installed PrettyTables ──────────────── v3.3.2 Installed CategoricalArrays ─────────── v0.10.7 Installed DocStringExtensions ───────── v0.9.5 Installed SeuratRDS ─────────────────── v1.0.3 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [dc2ff7d6] + SeuratRDS v1.0.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 ⌅ [324d7699] + CategoricalArrays v0.10.7 [34da2185] + Compat v4.18.1 [8f4d0f93] + Conda v1.10.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.5 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [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 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [e1d29d7a] + Missings v1.2.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [69de0a69] + Parsers v2.8.5 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [43287f4e] + PtrArrays v1.4.0 ⌅ [6f49c342] + RCall v0.13.18 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.10 [dc2ff7d6] + SeuratRDS v1.0.3 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.11 [4c63d2b9] + StatsFuns v2.1.0 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.4.4 [ec057cc2] + StructUtils v2.8.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [81def892] + VersionParsing v1.3.0 [1b915085] + WinReg v1.0.0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [0dad84c5] + ArgTools v1.2.0 [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 v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6/build.log` Installation completed after 244.64s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Project No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` Manifest No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling project... 282.8 s ✓ InlineStrings 0.6 s ✓ Reexport 1.0 s ✓ Statistics 1.0 s ✓ DataAPI 2.3 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.6 s ✓ StatsAPI 131.8 s ✓ OrderedCollections 49.5 s ✓ InvertedIndices 1.1 s ✓ DocStringExtensions 0.7 s ✓ ShiftedArrays 0.6 s ✓ VersionParsing 16.5 s ✓ WinReg 33.3 s ✓ PtrArrays 0.5 s ✓ IteratorInterfaceExtensions 35.9 s ✓ LaTeXStrings 2.0 s ✓ Crayons 1.1 s ✓ Requires 0.9 s ✓ DelimitedFiles 139.8 s ✓ SentinelArrays 2.8 s ✓ StructUtils 1.4 s ✓ Compat 2.4 s ✓ Preferences 36.7 s ✓ Statistics → SparseArraysExt 50.7 s ✓ Missings 21.5 s ✓ PooledArrays 1.5 s ✓ LogExpFunctions 35.4 s ✓ AliasTables 0.5 s ✓ TableTraits 0.6 s ✓ Compat → CompatLinearAlgebraExt 2.9 s ✓ JLLWrappers 2.6 s ✓ PrecompileTools 495.5 s ✓ CategoricalArrays 135.1 s ✓ Tables 238.4 s ✓ DataStructures 3.0 s ✓ Rmath_jll 3.1 s ✓ OpenSpecFun_jll 67.9 s ✓ StringManipulation 32.8 s ✓ Parsers 32.2 s ✓ StructUtils → StructUtilsTablesExt 34.8 s ✓ SortingAlgorithms 2.8 s ✓ Rmath 71.0 s ✓ SpecialFunctions 178.9 s ✓ PrettyTables 93.1 s ✓ JSON 53.8 s ✓ InlineStrings → ParsersExt  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ======================================================================================  cmd: /opt/julia/bin/julia 383 running 1 of 1  signal (10): User defined signal 1 int64hash at /source/src/support/hashing.c:35:9 bitmix at /source/src/support/hashing.h:31:12 [inlined] type_object_id_ at /source/src/builtins.c:419:13 jl_idset_peek_bp at /source/src/idset.c:34:20 jl_idset_get at /source/src/idset.c:40:19 jl_as_global_root at /source/src/staticdata.c:2747:24 [inlined] jl_as_global_root at /source/src/staticdata.c:2727:26 inst_datatype_inner at /source/src/jltypes.c:2451:22 jl_apply_tuple_type_v_ at /source/src/jltypes.c:2635:12 [inlined] ijl_apply_tuple_type_v at /source/src/jltypes.c:2645:12 _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] jl_f__apply_iterate at /source/src/builtins.c:905:26 argtypes_to_type at ./../usr/share/julia/Compiler/src/typeutils.jl:60:0 (pc: 162) handle_call! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1371:0 [inlined] assemble_inline_todo! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1615:0 (pc: 412) ssa_inlining_pass! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:76:0 [inlined] run_passes_ipo_safe at ./../usr/share/julia/Compiler/src/optimize.jl:1048:0 (pc: 8) run_passes_ipo_safe at ./../usr/share/julia/Compiler/src/optimize.jl:1061:0 [inlined] optimize at ./../usr/share/julia/Compiler/src/optimize.jl:1034:0 [inlined] finish_nocycle at ./../usr/share/julia/Compiler/src/typeinfer.jl:278:0 (pc: 14) jfptr_finish_nocycle_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4985:0 (pc: 251) typeinf_ext at ./../usr/share/julia/Compiler/src/typeinfer.jl:1537:0 (pc: 150) typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1742:0 [inlined] typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1751:0 (pc: 15) jfptr_typeinf_ext_toplevel_5.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] jl_type_infer at /source/src/gf.c:479:35 jl_compile_method_very_internal at /source/src/gf.c:3923:20 _jl_invoke at /source/src/gf.c:4352:16 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] ijl_lower at /source/src/ast.c:1274:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:31 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:706:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:897:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_eval_module_expr at /source/src/toplevel.c:263:5 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:665:27 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:325:0 (pc: 1) include_package_for_output at ./loading.jl:3296:0 (pc: 837) jfptr_include_package_for_output_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:706:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:897:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) include_string at ./loading.jl:3142:0 [inlined] exec_options at ./client.jl:353:0 (pc: 841) _start at ./client.jl:596:0 (pc: 294) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x75e240088249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file)   ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ==============================================================  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 240 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:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000079a8fe9291e0 Total snapshots: 380. Utilization: 0% ╎380 @Base/task.jl:1170 wait_forever() 379╎ 380 @Base/task.jl:1248 wait() ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== 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:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000070f7ab7e8880 Total snapshots: 325. Utilization: 0% ╎325 @Base/task.jl:1170 wait_forever() 324╎ 325 @Base/task.jl:1248 wait() [240] 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:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4360:23 [inlined] ijl_apply_generic at /source/src/gf.c:4598:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) Allocations: 4589926 (Pool: 4589761; Big: 165); GC: 7 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") error at ./error.jl:56:0 (pc: 6) PkgEval terminated after 2739.58s: test duration exceeded the time limit