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1.5.0-DEV-7206b56e94.log
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1.5.0-DEV-7206b56e94.log
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Julia Version 1.5.0-DEV.485
Commit 7206b56e94 (2020-03-18 17:25 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed CodecZlib ─────────── v0.7.0
Installed Zlib_jll ──────────── v1.2.11+8
Installed Combinatorics ─────── v0.7.0
Installed Libz ──────────────── v1.0.1
Installed FixedPointNumbers ─── v0.7.1
Installed ColorTypes ────────── v0.9.1
Installed YAML ──────────────── v0.4.0
Installed RecipesBase ───────── v0.8.0
Installed DataStructures ────── v0.17.10
Installed BioAlignments ─────── v1.0.1
Installed Polynomials ───────── v0.6.1
Installed BufferedStreams ───── v1.0.0
Installed URIParser ─────────── v0.4.0
Installed BGZFStreams ───────── v0.3.0
Installed Compat ────────────── v2.2.0
Installed Twiddle ───────────── v1.1.1
Installed IndexableBitVectors ─ v1.0.0
Installed BioSymbols ────────── v3.1.0
Installed Automa ────────────── v0.8.0
Installed GenomicFeatures ───── v1.0.4
Installed OrderedCollections ── v1.1.0
Installed TranscodingStreams ── v0.9.5
Installed BioCore ───────────── v2.0.5
Installed IntervalTrees ─────── v1.0.0
Installed BioSequences ──────── v1.1.0
#=#=# ##################################################### 74.2%######################################################################## 100.0%
Updating `~/.julia/environments/v1.5/Project.toml`
00701ae9 + BioAlignments v1.0.1
Updating `~/.julia/environments/v1.5/Manifest.toml`
67c07d97 + Automa v0.8.0
28d598bf + BGZFStreams v0.3.0
00701ae9 + BioAlignments v1.0.1
37cfa864 + BioCore v2.0.5
7e6ae17a + BioSequences v1.1.0
3c28c6f8 + BioSymbols v3.1.0
e1450e63 + BufferedStreams v1.0.0
944b1d66 + CodecZlib v0.7.0
3da002f7 + ColorTypes v0.9.1
861a8166 + Combinatorics v0.7.0
34da2185 + Compat v2.2.0
864edb3b + DataStructures v0.17.10
53c48c17 + FixedPointNumbers v0.7.1
899a7d2d + GenomicFeatures v1.0.4
1cb3b9ac + IndexableBitVectors v1.0.0
524e6230 + IntervalTrees v1.0.0
2ec943e9 + Libz v1.0.1
bac558e1 + OrderedCollections v1.1.0
f27b6e38 + Polynomials v0.6.1
3cdcf5f2 + RecipesBase v0.8.0
3bb67fe8 + TranscodingStreams v0.9.5
7200193e + Twiddle v1.1.1
30578b45 + URIParser v0.4.0
ddb6d928 + YAML v0.4.0
83775a58 + Zlib_jll v1.2.11+8
2a0f44e3 + Base64
ade2ca70 + Dates
8bb1440f + DelimitedFiles
8ba89e20 + Distributed
b77e0a4c + InteractiveUtils
76f85450 + LibGit2
8f399da3 + Libdl
37e2e46d + LinearAlgebra
56ddb016 + Logging
d6f4376e + Markdown
a63ad114 + Mmap
44cfe95a + Pkg
de0858da + Printf
9abbd945 + Profile
3fa0cd96 + REPL
9a3f8284 + Random
ea8e919c + SHA
9e88b42a + Serialization
1a1011a3 + SharedArrays
6462fe0b + Sockets
2f01184e + SparseArrays
10745b16 + Statistics
8dfed614 + Test
cf7118a7 + UUIDs
4ec0a83e + Unicode
Testing BioAlignments
Status `/tmp/jl_HPg5f9/Project.toml`
67c07d97 Automa v0.8.0
28d598bf BGZFStreams v0.3.0
00701ae9 BioAlignments v1.0.1
37cfa864 BioCore v2.0.5
7e6ae17a BioSequences v1.1.0
3c28c6f8 BioSymbols v3.1.0
e1450e63 BufferedStreams v1.0.0
899a7d2d GenomicFeatures v1.0.4
524e6230 IntervalTrees v1.0.0
ddb6d928 YAML v0.4.0
37e2e46d LinearAlgebra
de0858da Printf
8dfed614 Test
Status `/tmp/jl_HPg5f9/Manifest.toml`
67c07d97 Automa v0.8.0
28d598bf BGZFStreams v0.3.0
00701ae9 BioAlignments v1.0.1
37cfa864 BioCore v2.0.5
7e6ae17a BioSequences v1.1.0
3c28c6f8 BioSymbols v3.1.0
e1450e63 BufferedStreams v1.0.0
944b1d66 CodecZlib v0.7.0
3da002f7 ColorTypes v0.9.1
861a8166 Combinatorics v0.7.0
34da2185 Compat v2.2.0
864edb3b DataStructures v0.17.10
53c48c17 FixedPointNumbers v0.7.1
899a7d2d GenomicFeatures v1.0.4
1cb3b9ac IndexableBitVectors v1.0.0
524e6230 IntervalTrees v1.0.0
2ec943e9 Libz v1.0.1
bac558e1 OrderedCollections v1.1.0
f27b6e38 Polynomials v0.6.1
3cdcf5f2 RecipesBase v0.8.0
3bb67fe8 TranscodingStreams v0.9.5
7200193e Twiddle v1.1.1
30578b45 URIParser v0.4.0
ddb6d928 YAML v0.4.0
83775a58 Zlib_jll v1.2.11+8
2a0f44e3 Base64
ade2ca70 Dates
8bb1440f DelimitedFiles
8ba89e20 Distributed
b77e0a4c InteractiveUtils
76f85450 LibGit2
8f399da3 Libdl
37e2e46d LinearAlgebra
56ddb016 Logging
d6f4376e Markdown
a63ad114 Mmap
44cfe95a Pkg
de0858da Printf
9abbd945 Profile
3fa0cd96 REPL
9a3f8284 Random
ea8e919c SHA
9e88b42a Serialization
1a1011a3 SharedArrays
6462fe0b Sockets
2f01184e SparseArrays
10745b16 Statistics
8dfed614 Test
cf7118a7 UUIDs
4ec0a83e Unicode
julia: /workspace/srcdir/src/cgutils.cpp:679: llvm::Type* _julia_struct_to_llvm(jl_codegen_params_t*, jl_value_t*, jl_unionall_t*, bool*, bool): Assertion `isptr == jl_field_isptr(jst, i)' failed.
signal (6): Aborted
in expression starting at /home/pkgeval/.julia/packages/BioSymbols/8RyRT/src/aminoacid.jl:177
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f5208f09399)
__assert_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_julia_struct_to_llvm at /workspace/srcdir/src/cgutils.cpp:679
_julia_type_to_llvm at /workspace/srcdir/src/cgutils.cpp:555
julia_type_to_llvm at /workspace/srcdir/src/cgutils.cpp:565 [inlined]
typed_load at /workspace/srcdir/src/cgutils.cpp:1376
emit_builtin_call at /workspace/srcdir/src/codegen.cpp:2155
emit_call at /workspace/srcdir/src/codegen.cpp:2839
emit_expr at /workspace/srcdir/src/codegen.cpp:3602
emit_ssaval_assign at /workspace/srcdir/src/codegen.cpp:3304
emit_stmtpos at /workspace/srcdir/src/codegen.cpp:3498 [inlined]
emit_function at /workspace/srcdir/src/codegen.cpp:6113
jl_emit_code at /workspace/srcdir/src/codegen.cpp:6459
jl_emit_codeinst at /workspace/srcdir/src/codegen.cpp:6493
jl_compile_workqueue at /workspace/srcdir/src/codegen.cpp:6585
_jl_compile_codeinst at /workspace/srcdir/src/jitlayers.cpp:90
jl_generate_fptr at /workspace/srcdir/src/jitlayers.cpp:244
jl_compile_method_internal at /workspace/srcdir/src/gf.c:1902
jl_compile_method_internal at /workspace/srcdir/src/gf.c:1857 [inlined]
_jl_invoke at /workspace/srcdir/src/gf.c:2162 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2336
jl_apply at /workspace/srcdir/src/julia.h:1685 [inlined]
do_call at /workspace/srcdir/src/interpreter.c:369
eval_value at /workspace/srcdir/src/interpreter.c:458
eval_body at /workspace/srcdir/src/interpreter.c:680
jl_interpret_toplevel_thunk at /workspace/srcdir/src/interpreter.c:915
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:813
jl_parse_eval_all at /workspace/srcdir/src/ast.c:910
jl_load_rewrite at /workspace/srcdir/src/toplevel.c:874
include at ./Base.jl:380
include at ./Base.jl:368 [inlined]
include at /home/pkgeval/.julia/packages/BioSymbols/8RyRT/src/BioSymbols.jl:11
_jl_invoke at /workspace/srcdir/src/gf.c:2152 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2336
jl_apply at /workspace/srcdir/src/julia.h:1685 [inlined]
do_call at /workspace/srcdir/src/interpreter.c:369
eval_value at /workspace/srcdir/src/interpreter.c:458
eval_stmt_value at /workspace/srcdir/src/interpreter.c:409 [inlined]
eval_body at /workspace/srcdir/src/interpreter.c:821
jl_interpret_toplevel_thunk at /workspace/srcdir/src/interpreter.c:915
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:813
jl_eval_module_expr at /workspace/srcdir/src/toplevel.c:180
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:639
jl_parse_eval_all at /workspace/srcdir/src/ast.c:910
jl_load_rewrite at /workspace/srcdir/src/toplevel.c:874
include at ./Base.jl:380
include at ./Base.jl:368
_jl_invoke at /workspace/srcdir/src/gf.c:2152 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2336
jl_apply at /workspace/srcdir/src/julia.h:1685 [inlined]
do_call at /workspace/srcdir/src/interpreter.c:369
eval_value at /workspace/srcdir/src/interpreter.c:458
eval_stmt_value at /workspace/srcdir/src/interpreter.c:409 [inlined]
eval_body at /workspace/srcdir/src/interpreter.c:821
eval_body at /workspace/srcdir/src/interpreter.c:744
jl_interpret_toplevel_thunk at /workspace/srcdir/src/interpreter.c:915
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:813
jl_toplevel_eval_in at /workspace/srcdir/src/toplevel.c:843
eval at ./boot.jl:331 [inlined]
eval at ./client.jl:451
_jl_invoke at /workspace/srcdir/src/gf.c:2152 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2336
top-level scope at ./none:3
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:807
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:763
jl_toplevel_eval_in at /workspace/srcdir/src/toplevel.c:843
eval at ./boot.jl:331
_jl_invoke at /workspace/srcdir/src/gf.c:2152 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2336
exec_options at ./client.jl:264
_start at ./client.jl:490
jfptr__start_44182.clone_1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /workspace/srcdir/src/gf.c:2152 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2336
jl_apply at /workspace/srcdir/ui/../src/julia.h:1685 [inlined]
true_main at /workspace/srcdir/ui/repl.c:96
main at /workspace/srcdir/ui/repl.c:217
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4015e4)
Allocations: 7620350 (Pool: 7617982; Big: 2368); GC: 9
ERROR: LoadError: Failed to precompile BioSymbols [3c28c6f8-a34d-59c4-9654-267d177fcfa9] to /home/pkgeval/.julia/compiled/v1.5/BioSymbols/WGJJN_iHGXN.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1288
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::Function, ::Module, ::String) at ./Base.jl:380
[7] include(::Module, ::String) at ./Base.jl:368
[8] top-level scope at none:2
[9] eval at ./boot.jl:331 [inlined]
[10] eval(::Expr) at ./client.jl:451
[11] top-level scope at ./none:3
in expression starting at /home/pkgeval/.julia/packages/BioSequences/7i86L/src/BioSequences.jl:188
ERROR: LoadError: Failed to precompile BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] to /home/pkgeval/.julia/compiled/v1.5/BioSequences/i7zyu_iHGXN.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1288
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::Function, ::Module, ::String) at ./Base.jl:380
[7] include(::Module, ::String) at ./Base.jl:368
[8] top-level scope at none:2
[9] eval at ./boot.jl:331 [inlined]
[10] eval(::Expr) at ./client.jl:451
[11] top-level scope at ./none:3
in expression starting at /home/pkgeval/.julia/packages/BioAlignments/FOisL/src/BioAlignments.jl:89
ERROR: LoadError: Failed to precompile BioAlignments [00701ae9-d1dc-5365-b64a-a3a3ebf5695e] to /home/pkgeval/.julia/compiled/v1.5/BioAlignments/8o0Cp_iHGXN.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1288
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::String) at ./client.jl:441
[7] top-level scope at none:6
in expression starting at /home/pkgeval/.julia/packages/BioAlignments/FOisL/test/runtests.jl:2
ERROR: Package BioAlignments errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:53
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1523
[3] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:316
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:303
[5] #test#68 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[6] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[7] #test#67 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[8] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[10] test(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[11] top-level scope at none:13