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1.6.0-DEV-300e34cf74.log
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################################################################################
# PkgEval set-up: 2020-10-30T06:02:46.119
#
Julia Version 1.6.0-DEV.1380
Commit 300e34cf74 (2020-10-30 02:28 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: AMD EPYC 7502 32-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-11.0.0 (ORCJIT, znver2)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_MAX_NUM_PRECOMPILE_FILES = 9223372036854775807
################################################################################
# Installation: 2020-10-30T06:02:47.453
#
Resolving package versions...
Installed BGZFStreams ───────── v0.3.0
Installed Twiddle ───────────── v1.1.2
Installed BioCore ───────────── v2.0.5
Installed Automa ────────────── v0.7.0
Installed GeneticVariation ──── v0.4.0
Installed JLLWrappers ───────── v1.1.3
Installed BioSymbols ────────── v3.1.0
Installed BioSequences ──────── v1.1.0
Installed Zlib_jll ──────────── v1.2.11+18
Installed OrderedCollections ── v1.3.1
Installed RecipesBase ───────── v0.8.0
Installed CodecZlib ─────────── v0.7.0
Installed IndexableBitVectors ─ v1.0.0
Installed IntervalTrees ─────── v1.0.0
Installed DataStructures ────── v0.18.8
Installed Combinatorics ─────── v0.7.0
Installed TranscodingStreams ── v0.9.5
Installed BufferedStreams ───── v1.0.0
Installed Polynomials ───────── v0.6.1
Installed YAML ──────────────── v0.4.2
Installed Compat ────────────── v3.23.0
Updating `~/.julia/environments/v1.6/Project.toml`
[9bc6ac9d] + GeneticVariation v0.4.0
Updating `~/.julia/environments/v1.6/Manifest.toml`
[67c07d97] + Automa v0.7.0
[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 v3.23.0
[864edb3b] + DataStructures v0.18.8
[9bc6ac9d] + GeneticVariation v0.4.0
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[692b3bcd] + JLLWrappers v1.1.3
[bac558e1] + OrderedCollections v1.3.1
[f27b6e38] + Polynomials v0.6.1
[3cdcf5f2] + RecipesBase v0.8.0
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.2
[ddb6d928] + YAML v0.4.2
[83775a58] + Zlib_jll v1.2.11+18
[0dad84c5] + ArgTools
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[f43a241f] + Downloads
[b77e0a4c] + InteractiveUtils
[b27032c2] + LibCURL
[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
[fa267f1f] + TOML
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[deac9b47] + LibCURL_jll
[14a3606d] + MozillaCACerts_jll
################################################################################
# Testing: 2020-10-30T06:02:51.154
#
┌ Warning: using test/REQUIRE files is deprecated and current support is lacking in some areas
└ @ Pkg.Operations /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1547
Testing GeneticVariation
Status `/tmp/jl_tcmUP4/Project.toml`
[67c07d97] Automa v0.7.0
[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 v1.1.2
[ddb6d928] YAML v0.4.2
[8dfed614] Test
Status `/tmp/jl_tcmUP4/Manifest.toml`
[67c07d97] Automa v0.7.0
[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 v3.23.0
[864edb3b] DataStructures v0.18.8
[9bc6ac9d] GeneticVariation v0.4.0
[1cb3b9ac] IndexableBitVectors v1.0.0
[524e6230] IntervalTrees v1.0.0
[692b3bcd] JLLWrappers v1.1.3
[bac558e1] OrderedCollections v1.3.1
[f27b6e38] Polynomials v0.6.1
[3cdcf5f2] RecipesBase v0.8.0
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.2
[ddb6d928] YAML v0.4.2
[83775a58] Zlib_jll v1.2.11+18
[0dad84c5] ArgTools
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[f43a241f] Downloads
[b77e0a4c] InteractiveUtils
[b27032c2] LibCURL
[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
[fa267f1f] TOML
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[deac9b47] LibCURL_jll
[14a3606d] MozillaCACerts_jll
Testing Running tests...
[ Info: Compiling VCF parser...
Cloning into '/home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens'...
Note: switching to '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 switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
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_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
PkgEval succeeded
################################################################################
# PkgEval teardown: 2020-10-30T06:04:42.780
CPU usage: 115.07s (110.56s user, 4.72s kernel)
Network usage:
- eth0: 5.881 MiB received, 85.406 KiB sent
Raw statistics: {"blkio_stats":{"io_queue_recursive":[],"io_serviced_recursive":[{"major":259,"value":0,"op":"Read","minor":0},{"major":259,"value":5,"op":"Write","minor":0},{"major":259,"value":0,"op":"Sync","minor":0},{"major":259,"value":5,"op":"Async","minor":0},{"major":259,"value":5,"op":"Total","minor":0},{"major":253,"value":0,"op":"Read","minor":2},{"major":253,"value":5,"op":"Write","minor":2},{"major":253,"value":0,"op":"Sync","minor":2},{"major":253,"value":5,"op":"Async","minor":2},{"major":253,"value":5,"op":"Total","minor":2}],"io_time_recursive":[],"sectors_recursive":[],"io_service_bytes_recursive":[{"major":259,"value":0,"op":"Read","minor":0},{"major":259,"value":28672,"op":"Write","minor":0},{"major":259,"value":0,"op":"Sync","minor":0},{"major":259,"value":28672,"op":"Async","minor":0},{"major":259,"value":28672,"op":"Total","minor":0},{"major":253,"value":0,"op":"Read","minor":2},{"major":253,"value":28672,"op":"Write","minor":2},{"major":253,"value":0,"op":"Sync","minor":2},{"major":253,"value":28672,"op":"Async","minor":2},{"major":253,"value":28672,"op":"Total","minor":2}],"io_wait_time_recursive":[],"io_merged_recursive":[],"io_service_time_recursive":[]},"memory_stats":{"usage":237563904,"max_usage":1041584128,"stats":{"hierarchical_memory_limit":9223372036854771712,"pgmajfault":0,"total_rss":200777728,"inactive_file":8192,"inactive_anon":4612096,"total_pgfault":1651053,"total_cache":30003200,"total_rss_huge":0,"total_active_anon":226156544,"total_pgmajfault":0,"pgpgin":921461,"rss_huge":0,"mapped_file":0,"total_inactive_file":8192,"dirty":0,"total_unevictable":0,"total_dirty":0,"writeback":0,"pgpgout":865118,"hierarchical_memsw_limit":0,"cache":30003200,"active_file":0,"pgfault":1651053,"total_mapped_file":0,"total_pgpgout":865118,"total_writeback":0,"rss":200777728,"unevictable":0,"total_inactive_anon":4612096,"total_pgpgin":921461,"active_anon":226156544,"total_active_file":0},"limit":540972998656},"name":"/GeneticVariation-q3d5DjPE","networks":{"eth0":{"rx_bytes":6166397,"rx_packets":1097,"tx_packets":714,"tx_bytes":87456,"tx_dropped":0,"rx_dropped":4,"tx_errors":0,"rx_errors":0}},"id":"5e5c79a2466b1bdb1f55f2c9a359df20a6e3abec95ee626d23df5d57dd3b230f","preread":"0001-01-01T00:00:00Z","storage_stats":{},"precpu_stats":{"throttling_data":{"throttled_periods":0,"throttled_time":0,"periods":0},"cpu_usage":{"usage_in_usermode":0,"usage_in_kernelmode":0,"total_usage":0}},"pids_stats":{"current":38},"num_procs":0,"cpu_stats":{"throttling_data":{"throttled_periods":0,"throttled_time":0,"periods":0},"system_cpu_usage":113594565900000000,"online_cpus":128,"cpu_usage":{"usage_in_usermode":110560000000,"usage_in_kernelmode":4720000000,"total_usage":115074664331,"percpu_usage":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9100,115074648911,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6320,0,0,0,0,0,0,0,0,0]}},"read":"2020-10-30T06:04:42.832741973Z"}