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1.5.0-DEV-ed177d17d6.log
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Julia Version 1.5.0-DEV.158
Commit ed177d17d6 (2020-01-27 16:45 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-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed SortingAlgorithms ─────────── v0.3.1
Installed MsgPack ───────────────────── v0.2.0
Installed Parsers ───────────────────── v0.3.10
Installed IndexableBitVectors ───────── v1.0.0
Installed BufferedStreams ───────────── v1.0.0
Installed BioStructures ─────────────── v0.9.1
Installed BioAlignments ─────────────── v1.0.1
Installed GenomicFeatures ───────────── v1.0.4
Installed Compat ────────────────────── v2.2.0
Installed Tables ────────────────────── v0.2.11
Installed BinaryProvider ────────────── v0.5.8
Installed OrderedCollections ────────── v1.1.0
Installed URIParser ─────────────────── v0.4.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed Combinatorics ─────────────── v0.7.0
Installed ColorTypes ────────────────── v0.9.1
Installed CodecZlib ─────────────────── v0.6.0
Installed DataValueInterfaces ───────── v1.0.0
Installed FileIO ────────────────────── v1.2.1
Installed DataStructures ────────────── v0.17.9
Installed BGZFStreams ───────────────── v0.3.0
Installed Polynomials ───────────────── v0.6.0
Installed BioSequences ──────────────── v1.1.0
Installed MetaGraphs ────────────────── v0.6.4
Installed FixedPointNumbers ─────────── v0.7.1
Installed JLD2 ──────────────────────── v0.1.11
Installed BioCore ───────────────────── v2.0.5
Installed Missings ──────────────────── v0.4.3
Installed Inflate ───────────────────── v0.1.1
Installed ArnoldiMethod ─────────────── v0.0.4
Installed StaticArrays ──────────────── v0.12.1
Installed LightGraphs ───────────────── v1.3.0
Installed MMTF ──────────────────────── v0.1.0
Installed Format ────────────────────── v1.1.0
Installed Twiddle ───────────────────── v1.1.1
Installed JSON ──────────────────────── v0.21.0
Installed TableTraits ───────────────── v1.0.0
Installed BioSymbols ────────────────── v3.1.0
Installed CategoricalArrays ─────────── v0.7.7
Installed DataAPI ───────────────────── v1.1.0
Installed YAML ──────────────────────── v0.3.2
Installed PooledArrays ──────────────── v0.5.3
Installed Automa ────────────────────── v0.8.0
Installed InvertedIndices ───────────── v1.0.0
Installed DataFrames ────────────────── v0.20.0
Installed TranscodingStreams ────────── v0.9.5
Installed MacroTools ────────────────── v0.5.3
Installed RecipesBase ───────────────── v0.7.0
Installed SimpleTraits ──────────────── v0.9.1
Installed Libz ──────────────────────── v1.0.1
Installed IntervalTrees ─────────────── v1.0.0
Installed Reexport ──────────────────── v0.2.0
Installed Codecs ────────────────────── v0.5.0
Updating `~/.julia/environments/v1.5/Project.toml`
[de9282ab] + BioStructures v0.9.1
Updating `~/.julia/environments/v1.5/Manifest.toml`
[ec485272] + ArnoldiMethod v0.0.4
[67c07d97] + Automa v0.8.0
[28d598bf] + BGZFStreams v0.3.0
[b99e7846] + BinaryProvider v0.5.8
[00701ae9] + BioAlignments v1.0.1
[37cfa864] + BioCore v2.0.5
[7e6ae17a] + BioSequences v1.1.0
[de9282ab] + BioStructures v0.9.1
[3c28c6f8] + BioSymbols v3.1.0
[e1450e63] + BufferedStreams v1.0.0
[324d7699] + CategoricalArrays v0.7.7
[944b1d66] + CodecZlib v0.6.0
[19ecbf4d] + Codecs v0.5.0
[3da002f7] + ColorTypes v0.9.1
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.20.0
[864edb3b] + DataStructures v0.17.9
[e2d170a0] + DataValueInterfaces v1.0.0
[5789e2e9] + FileIO v1.2.1
[53c48c17] + FixedPointNumbers v0.7.1
[1fa38f19] + Format v1.1.0
[899a7d2d] + GenomicFeatures v1.0.4
[1cb3b9ac] + IndexableBitVectors v1.0.0
[d25df0c9] + Inflate v0.1.1
[524e6230] + IntervalTrees v1.0.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[033835bb] + JLD2 v0.1.11
[682c06a0] + JSON v0.21.0
[2ec943e9] + Libz v1.0.1
[093fc24a] + LightGraphs v1.3.0
[259c3a9c] + MMTF v0.1.0
[1914dd2f] + MacroTools v0.5.3
[626554b9] + MetaGraphs v0.6.4
[e1d29d7a] + Missings v0.4.3
[99f44e22] + MsgPack v0.2.0
[bac558e1] + OrderedCollections v1.1.0
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.3
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[699a6c99] + SimpleTraits v0.9.1
[a2af1166] + SortingAlgorithms v0.3.1
[90137ffa] + StaticArrays v0.12.1
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.1
[30578b45] + URIParser v0.4.0
[ddb6d928] + YAML v0.3.2
[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
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building CodecZlib → `~/.julia/packages/CodecZlib/5t9zO/deps/build.log`
Updating `/tmp/jl_kVuOh8/Project.toml`
[no changes]
Updating `/tmp/jl_kVuOh8/Manifest.toml`
[no changes]
Testing BioStructures
Updating `/tmp/jl_FOYjFR/Project.toml`
[no changes]
Updating `/tmp/jl_FOYjFR/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_FOYjFR/Project.toml`
[00701ae9] BioAlignments v1.0.1
[37cfa864] BioCore v2.0.5
[7e6ae17a] BioSequences v1.1.0
[de9282ab] BioStructures v0.9.1
[3c28c6f8] BioSymbols v3.1.0
[944b1d66] CodecZlib v0.6.0
[a93c6f00] DataFrames v0.20.0
[1fa38f19] Format v1.1.0
[093fc24a] LightGraphs v1.3.0
[259c3a9c] MMTF v0.1.0
[626554b9] MetaGraphs v0.6.4
[3cdcf5f2] RecipesBase v0.7.0
[37e2e46d] LinearAlgebra
[10745b16] Statistics
[8dfed614] Test
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
[ Info: Skipping download tests on Linux due to timeouts during CI; change skip_linux_download in test/runtests.jl to run these tests
Test Summary: |
PDB interface | No tests
Test Summary: | Pass Total
Types | 313 313
Test Summary: | Pass Total
PDB reading | 399 399
Test Summary: | Pass Total
PDB writing | 117 117
Test Summary: | Pass Total
mmCIF | 257 257
Test Summary: | Pass Total
MMTF | 260 260
[ Info: Superimposing based on a sequence alignment between 51 residues
[ Info: Superimposing based on 51 atoms
[ Info: Superimposing based on a sequence alignment between 51 residues
[ Info: Superimposing based on 51 atoms
[ Info: Superimposing based on a sequence alignment between 30 residues
[ Info: Superimposing based on 30 atoms
[ Info: Superimposing based on a sequence alignment between 30 residues
[ Info: Superimposing based on 30 atoms
[ Info: Superimposing based on a sequence alignment between 51 residues
[ Info: Superimposing based on 51 atoms
[ Info: Superimposing based on a sequence alignment between 51 residues
[ Info: Superimposing based on 51 atoms
[ Info: Superimposing based on a sequence alignment between 51 residues
[ Info: Superimposing based on 51 atoms
[ Info: Superimposing based on a sequence alignment between 51 residues
[ Info: Superimposing based on 51 atoms
Test Summary: | Pass Total
Spatial | 113 113
Testing BioStructures tests passed