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1.5.0-DEV-1f787492c3.log
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1.5.0-DEV-1f787492c3.log
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Julia Version 1.5.0-DEV.507
Commit 1f787492c3 (2020-03-25 15:03 UTC)
Platform Info:
OS: Linux (x86_64-pc-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 Combinatorics ─────── v0.7.0
Installed RecipesBase ───────── v0.8.0
Installed OrderedCollections ── v1.1.0
Installed BioCore ───────────── v2.0.5
Installed BioSymbols ────────── v3.1.0
Installed IntervalTrees ─────── v1.0.0
Installed Automa ────────────── v0.8.0
Installed GeneticVariation ──── v0.4.0
Installed BGZFStreams ───────── v0.3.0
Installed Zlib_jll ──────────── v1.2.11+8
Installed YAML ──────────────── v0.4.0
Installed CodecZlib ─────────── v0.7.0
Installed Compat ────────────── v3.8.0
Installed Twiddle ───────────── v1.1.1
Installed TranscodingStreams ── v0.9.5
Installed IndexableBitVectors ─ v1.0.0
Installed BioSequences ──────── v1.1.0
Installed DataStructures ────── v0.17.10
Installed Polynomials ───────── v0.6.1
Installed BufferedStreams ───── v1.0.0
Updating `~/.julia/environments/v1.5/Project.toml`
9bc6ac9d + GeneticVariation v0.4.0
Updating `~/.julia/environments/v1.5/Manifest.toml`
67c07d97 + Automa v0.8.0
28d598bf + BGZFStreams v0.3.0
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
861a8166 + Combinatorics v0.7.0
34da2185 + Compat v3.8.0
864edb3b + DataStructures v0.17.10
9bc6ac9d + GeneticVariation v0.4.0
1cb3b9ac + IndexableBitVectors v1.0.0
524e6230 + IntervalTrees v1.0.0
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
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
┌ Warning: using test/REQUIRE files is deprecated and current support is lacking in some areas
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1433
Testing GeneticVariation
Status `/tmp/jl_f33PWp/Project.toml`
67c07d97 Automa v0.8.0
28d598bf BGZFStreams v0.3.0
37cfa864 BioCore v2.0.5
7e6ae17a BioSequences v1.1.0
e1450e63 BufferedStreams v1.0.0
861a8166 Combinatorics v0.7.0
9bc6ac9d GeneticVariation v0.4.0
524e6230 IntervalTrees v1.0.0
7200193e Twiddle v1.1.1
ddb6d928 YAML v0.4.0
8dfed614 Test
Status `/tmp/jl_f33PWp/Manifest.toml`
67c07d97 Automa v0.8.0
28d598bf BGZFStreams v0.3.0
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
861a8166 Combinatorics v0.7.0
34da2185 Compat v3.8.0
864edb3b DataStructures v0.17.10
9bc6ac9d GeneticVariation v0.4.0
1cb3b9ac IndexableBitVectors v1.0.0
524e6230 IntervalTrees v1.0.0
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
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
[ Info: Compiling VCF parser...
Cloning into '/home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens'...
Note: checking out 'v1.0.0-9-ga88ddc9'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b <new-branch-name>
HEAD is now at a88ddc9 Merge pull request #29 from jgreener64/mmtf
Test Summary: | Pass Total
VCF | 165 165
Test Summary: | Pass Total
BCF | 39 39
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead
│ caller = bp_chunk_count at site_counting.jl:96 [inlined]
└ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
┌ Warning: count_one_nibbles is deprecated, use count_1111_nibbles instead
│ caller = bp_chunk_count at site_counting.jl:80 [inlined]
└ @ Core ~/.julia/packages/GeneticVariation/r8DAL/src/site_counting.jl:80
Test Summary: | Pass Total
Site counting | 348 348
Test Summary: | Pass Total
MASH distances | 3 3
Test Summary: | Pass Total
Allele frequenies | 6 6
Test Summary: | Pass Total
Diversity Measures | 3 3
Test Summary: | Pass Total
Segregating sites | 2 2
Testing GeneticVariation tests passed