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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 SortingAlgorithms ──────────── v0.3.1
Installed DataValueInterfaces ────────── v1.0.0
Installed DataStreams ────────────────── v0.4.2
Installed BioServices ────────────────── v0.3.2
Installed AbstractTrees ──────────────── v0.3.2
Installed CategoricalArrays ──────────── v0.7.7
Installed DataFrames ─────────────────── v0.20.2
Installed BioMedQuery ────────────────── v0.6.6
Installed MariaDB_Connector_C_jll ────── v3.1.6+0
Installed WeakRefStrings ─────────────── v0.6.2
Installed MbedTLS_jll ────────────────── v2.16.0+1
Installed Zlib_jll ───────────────────── v1.2.11+8
Installed XML2_jll ───────────────────── v2.9.9+1
Installed LibCURL_jll ────────────────── v7.68.0+0
Installed JSON ───────────────────────── v0.21.0
Installed DataStructures ─────────────── v0.17.10
Installed IterTools ──────────────────── v1.3.0
Installed LightXML ───────────────────── v0.8.1
Installed CompilerSupportLibraries_jll ─ v0.3.0+0
Installed Reexport ───────────────────── v0.2.0
Installed InvertedIndices ────────────── v1.0.0
Installed PooledArrays ───────────────── v0.5.3
Installed SpecialFunctions ───────────── v0.9.0
Installed SQLite_jll ─────────────────── v3.31.1+0
Installed DataAPI ────────────────────── v1.1.0
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed Parsers ────────────────────── v0.3.12
Installed DecFP ──────────────────────── v0.4.10
Installed BinaryProvider ─────────────── v0.5.8
Installed FTPClient ──────────────────── v1.0.1
Installed OpenSSL_jll ────────────────── v1.1.1+1
Installed IniFile ────────────────────── v0.5.0
Installed Missings ───────────────────── v0.4.3
Installed XMLDict ────────────────────── v0.4.0
Installed DBInterface ────────────────── v2.0.0
Installed IteratorInterfaceExtensions ── v1.0.0
Installed EzXML ──────────────────────── v1.1.0
Installed SQLite ─────────────────────── v1.0.3
Installed Tables ─────────────────────── v1.0.3
Installed HTTP ───────────────────────── v0.8.12
Installed CSV ────────────────────────── v0.5.26
Installed URIParser ──────────────────── v0.4.0
Installed LibCURL ────────────────────── v0.5.2
Installed Gumbo ──────────────────────── v0.7.0
Installed LibSSH2_jll ────────────────── v1.9.0+1
Installed FilePathsBase ──────────────── v0.7.0
Installed Compat ─────────────────────── v3.8.0
Installed MySQL ──────────────────────── v1.0.1
Installed MbedTLS ────────────────────── v1.0.1
Installed Libiconv_jll ───────────────── v1.16.0+1
Installed TableTraits ────────────────── v1.0.0
Installed OrderedCollections ─────────── v1.1.0
#=#=# ######################################################################## 100.0%
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#=#=# ## 3.1%####### 10.0%############# 18.3%###################### 30.7%################################ 45.1%############################################## 65.1%################################################################ 88.9%######################################################################## 100.0%
#=#=# #### 5.9%############ 16.9%###################### 31.9%##################################### 51.8%######################################################## 78.6%######################################################################## 100.0%
#=#=# ############################## 42.2%######################################################################## 100.0%
#=#=# 0.8%############ 18.0%############################ 39.7%#################################################### 72.6%######################################################################## 100.0%
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#=#=# ############################## 42.2%############################### 44.0%######################################################################## 100.0%
Updating `~/.julia/environments/v1.5/Project.toml`
e96904bf + BioMedQuery v0.6.6
Updating `~/.julia/environments/v1.5/Manifest.toml`
1520ce14 + AbstractTrees v0.3.2
b99e7846 + BinaryProvider v0.5.8
e96904bf + BioMedQuery v0.6.6
a0d4ced5 + BioServices v0.3.2
336ed68f + CSV v0.5.26
324d7699 + CategoricalArrays v0.7.7
34da2185 + Compat v3.8.0
e66e0078 + CompilerSupportLibraries_jll v0.3.0+0
a10d1c49 + DBInterface v2.0.0
9a962f9c + DataAPI v1.1.0
a93c6f00 + DataFrames v0.20.2
9a8bc11e + DataStreams v0.4.2
864edb3b + DataStructures v0.17.10
e2d170a0 + DataValueInterfaces v1.0.0
55939f99 + DecFP v0.4.10
8f5d6c58 + EzXML v1.1.0
01fcc997 + FTPClient v1.0.1
48062228 + FilePathsBase v0.7.0
708ec375 + Gumbo v0.7.0
cd3eb016 + HTTP v0.8.12
83e8ac13 + IniFile v0.5.0
41ab1584 + InvertedIndices v1.0.0
c8e1da08 + IterTools v1.3.0
82899510 + IteratorInterfaceExtensions v1.0.0
682c06a0 + JSON v0.21.0
b27032c2 + LibCURL v0.5.2
deac9b47 + LibCURL_jll v7.68.0+0
29816b5a + LibSSH2_jll v1.9.0+1
94ce4f54 + Libiconv_jll v1.16.0+1
9c8b4983 + LightXML v0.8.1
aabc7e14 + MariaDB_Connector_C_jll v3.1.6+0
739be429 + MbedTLS v1.0.1
c8ffd9c3 + MbedTLS_jll v2.16.0+1
e1d29d7a + Missings v0.4.3
39abe10b + MySQL v1.0.1
458c3c95 + OpenSSL_jll v1.1.1+1
efe28fd5 + OpenSpecFun_jll v0.5.3+3
bac558e1 + OrderedCollections v1.1.0
69de0a69 + Parsers v0.3.12
2dfb63ee + PooledArrays v0.5.3
189a3867 + Reexport v0.2.0
0aa819cd + SQLite v1.0.3
76ed43ae + SQLite_jll v3.31.1+0
a2af1166 + SortingAlgorithms v0.3.1
276daf66 + SpecialFunctions v0.9.0
3783bdb8 + TableTraits v1.0.0
bd369af6 + Tables v1.0.3
30578b45 + URIParser v0.4.0
ea10d353 + WeakRefStrings v0.6.2
02c8fc9c + XML2_jll v2.9.9+1
228000da + XMLDict v0.4.0
83775a58 + Zlib_jll v1.2.11+8
2a0f44e3 + Base64
ade2ca70 + Dates
8bb1440f + DelimitedFiles
8ba89e20 + Distributed
9fa8497b + Future
b77e0a4c + InteractiveUtils
76f85450 + LibGit2
8f399da3 + Libdl
37e2e46d + LinearAlgebra
56ddb016 + Logging
d6f4376e + Markdown
a63ad114 + Mmap
44cfe95a + Pkg
de0858da + Printf
3fa0cd96 + REPL
9a3f8284 + Random
ea8e919c + SHA
9e88b42a + Serialization
1a1011a3 + SharedArrays
6462fe0b + Sockets
2f01184e + SparseArrays
10745b16 + Statistics
8dfed614 + Test
cf7118a7 + UUIDs
4ec0a83e + Unicode
Building LightXML → `~/.julia/packages/LightXML/W8FVT/deps/build.log`
Building DecFP ───→ `~/.julia/packages/DecFP/quvcm/deps/build.log`
Building SQLite ──→ `~/.julia/packages/SQLite/KwDwo/deps/build.log`
Building MySQL ───→ `~/.julia/packages/MySQL/8fJ1I/deps/build.log`
Building Gumbo ───→ `~/.julia/packages/Gumbo/OhZJu/deps/build.log`
Building LibCURL ─→ `~/.julia/packages/LibCURL/lWJxD/deps/build.log`
Testing BioMedQuery
Status `/tmp/jl_Z62UQk/Project.toml`
e96904bf BioMedQuery v0.6.6
a0d4ced5 BioServices v0.3.2
336ed68f CSV v0.5.26
a93c6f00 DataFrames v0.20.2
9a8bc11e DataStreams v0.4.2
01fcc997 FTPClient v1.0.1
cd3eb016 HTTP v0.8.12
9c8b4983 LightXML v0.8.1
739be429 MbedTLS v1.0.1
39abe10b MySQL v1.0.1
0aa819cd SQLite v1.0.3
228000da XMLDict v0.4.0
a5390f91 ZipFile v0.9.1
ade2ca70 Dates
8ba89e20 Distributed
2f01184e SparseArrays
8dfed614 Test
Status `/tmp/jl_Z62UQk/Manifest.toml`
1520ce14 AbstractTrees v0.3.2
b99e7846 BinaryProvider v0.5.8
e96904bf BioMedQuery v0.6.6
a0d4ced5 BioServices v0.3.2
336ed68f CSV v0.5.26
324d7699 CategoricalArrays v0.7.7
34da2185 Compat v3.8.0
e66e0078 CompilerSupportLibraries_jll v0.3.0+0
a10d1c49 DBInterface v2.0.0
9a962f9c DataAPI v1.1.0
a93c6f00 DataFrames v0.20.2
9a8bc11e DataStreams v0.4.2
864edb3b DataStructures v0.17.10
e2d170a0 DataValueInterfaces v1.0.0
55939f99 DecFP v0.4.10
8f5d6c58 EzXML v1.1.0
01fcc997 FTPClient v1.0.1
48062228 FilePathsBase v0.7.0
708ec375 Gumbo v0.7.0
cd3eb016 HTTP v0.8.12
83e8ac13 IniFile v0.5.0
41ab1584 InvertedIndices v1.0.0
c8e1da08 IterTools v1.3.0
82899510 IteratorInterfaceExtensions v1.0.0
682c06a0 JSON v0.21.0
b27032c2 LibCURL v0.5.2
deac9b47 LibCURL_jll v7.68.0+0
29816b5a LibSSH2_jll v1.9.0+1
94ce4f54 Libiconv_jll v1.16.0+1
9c8b4983 LightXML v0.8.1
aabc7e14 MariaDB_Connector_C_jll v3.1.6+0
739be429 MbedTLS v1.0.1
c8ffd9c3 MbedTLS_jll v2.16.0+1
e1d29d7a Missings v0.4.3
39abe10b MySQL v1.0.1
458c3c95 OpenSSL_jll v1.1.1+1
efe28fd5 OpenSpecFun_jll v0.5.3+3
bac558e1 OrderedCollections v1.1.0
69de0a69 Parsers v0.3.12
2dfb63ee PooledArrays v0.5.3
189a3867 Reexport v0.2.0
0aa819cd SQLite v1.0.3
76ed43ae SQLite_jll v3.31.1+0
a2af1166 SortingAlgorithms v0.3.1
276daf66 SpecialFunctions v0.9.0
3783bdb8 TableTraits v1.0.0
bd369af6 Tables v1.0.3
30578b45 URIParser v0.4.0
ea10d353 WeakRefStrings v0.6.2
02c8fc9c XML2_jll v2.9.9+1
228000da XMLDict v0.4.0
a5390f91 ZipFile v0.9.1
83775a58 Zlib_jll v1.2.11+8
2a0f44e3 Base64
ade2ca70 Dates
8bb1440f DelimitedFiles
8ba89e20 Distributed
9fa8497b Future
b77e0a4c InteractiveUtils
76f85450 LibGit2
8f399da3 Libdl
37e2e46d LinearAlgebra
56ddb016 Logging
d6f4376e Markdown
a63ad114 Mmap
44cfe95a Pkg
de0858da Printf
3fa0cd96 REPL
9a3f8284 Random
ea8e919c SHA
9e88b42a Serialization
1a1011a3 SharedArrays
6462fe0b Sockets
2f01184e SparseArrays
10745b16 Statistics
8dfed614 Test
cf7118a7 UUIDs
4ec0a83e Unicode
ERROR: LoadError: LoadError: LoadError: UndefVarError: MySQLHandle not defined
Stacktrace:
[1] getproperty(::Module, ::Symbol) at ./Base.jl:26
[2] top-level scope at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/DBUtils/mysql_db_utils.jl:55
[3] include(::Function, ::Module, ::String) at ./Base.jl:380
[4] include at ./Base.jl:368 [inlined]
[5] include(::String) at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/BioMedQuery.jl:4
[6] top-level scope at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/DBUtils/DBUtils.jl:4
[7] include(::Function, ::Module, ::String) at ./Base.jl:380
[8] include at ./Base.jl:368 [inlined]
[9] include(::String) at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/BioMedQuery.jl:4
[10] top-level scope at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/BioMedQuery.jl:21
[11] include(::Function, ::Module, ::String) at ./Base.jl:380
[12] include(::Module, ::String) at ./Base.jl:368
[13] top-level scope at none:2
[14] eval at ./boot.jl:331 [inlined]
[15] eval(::Expr) at ./client.jl:451
[16] top-level scope at ./none:3
in expression starting at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/DBUtils/mysql_db_utils.jl:55
in expression starting at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/DBUtils/DBUtils.jl:4
in expression starting at /home/pkgeval/.julia/packages/BioMedQuery/HCDqv/src/BioMedQuery.jl:21
ERROR: LoadError: Failed to precompile BioMedQuery [e96904bf-1073-5077-9b57-b0ce0ff5555a] to /home/pkgeval/.julia/compiled/v1.5/BioMedQuery/I7mWp_wFZxR.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/BioMedQuery/HCDqv/test/runtests.jl:12
ERROR: Package BioMedQuery 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