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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 Reexport ──────────────────── v0.2.0
Installed Combinatorics ─────────────── v0.7.0
Installed SortingAlgorithms ─────────── v0.3.1
Installed RecipesBase ───────────────── v0.8.0
Installed OrderedCollections ────────── v1.1.0
Installed ColorTypes ────────────────── v0.9.1
Installed Tables ────────────────────── v1.0.3
Installed BioStructures ─────────────── v0.9.3
Installed Missings ──────────────────── v0.4.3
Installed IntervalTrees ─────────────── v1.0.0
Installed BioCore ───────────────────── v2.0.5
Installed DataAPI ───────────────────── v1.1.0
Installed Parsers ───────────────────── v0.3.12
Installed BioSymbols ────────────────── v3.1.0
Installed FileIO ────────────────────── v1.2.4
Installed Automa ────────────────────── v0.8.0
Installed SimpleTraits ──────────────── v0.9.1
Installed Twiddle ───────────────────── v1.1.1
Installed Inflate ───────────────────── v0.1.2
Installed BGZFStreams ───────────────── v0.3.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed URIParser ─────────────────── v0.4.0
Installed TableTraits ───────────────── v1.0.0
Installed ArnoldiMethod ─────────────── v0.0.4
Installed MMTF ──────────────────────── v0.1.0
Installed IndexableBitVectors ───────── v1.0.0
Installed YAML ──────────────────────── v0.4.0
Installed Format ────────────────────── v1.1.0
Installed StaticArrays ──────────────── v0.12.1
Installed BinaryProvider ────────────── v0.5.8
Installed CategoricalArrays ─────────── v0.7.7
Installed GenomicFeatures ───────────── v1.0.4
Installed BioSequences ──────────────── v1.1.0
Installed LightGraphs ───────────────── v1.3.1
Installed MetaGraphs ────────────────── v0.6.5
Installed Compat ────────────────────── v2.2.0
Installed InvertedIndices ───────────── v1.0.0
Installed DataValueInterfaces ───────── v1.0.0
Installed PooledArrays ──────────────── v0.5.3
Installed Libz ──────────────────────── v1.0.1
Installed TranscodingStreams ────────── v0.9.5
Installed JLD2 ──────────────────────── v0.1.12
Installed DataFrames ────────────────── v0.20.2
Installed DataStructures ────────────── v0.17.10
Installed FixedPointNumbers ─────────── v0.7.1
Installed MacroTools ────────────────── v0.5.5
Installed MsgPack ───────────────────── v0.2.0
Installed CodecZlib ─────────────────── v0.6.0
Installed Polynomials ───────────────── v0.6.1
Installed BufferedStreams ───────────── v1.0.0
Installed BioAlignments ─────────────── v1.0.1
Installed JSON ──────────────────────── v0.21.0
Updating `~/.julia/environments/v1.5/Project.toml`
de9282ab + BioStructures v0.9.3
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 v0.9.3
3c28c6f8 + BioSymbols v3.1.0
e1450e63 + BufferedStreams v1.0.0
324d7699 + CategoricalArrays v0.7.7
944b1d66 + CodecZlib v0.6.0
3da002f7 + ColorTypes v0.9.1
861a8166 + Combinatorics v0.7.0
34da2185 + Compat v2.2.0
9a962f9c + DataAPI v1.1.0
a93c6f00 + DataFrames v0.20.2
864edb3b + DataStructures v0.17.10
e2d170a0 + DataValueInterfaces v1.0.0
5789e2e9 + FileIO v1.2.4
53c48c17 + FixedPointNumbers v0.7.1
1fa38f19 + Format v1.1.0
899a7d2d + GenomicFeatures v1.0.4
1cb3b9ac + IndexableBitVectors v1.0.0
d25df0c9 + Inflate v0.1.2
524e6230 + IntervalTrees v1.0.0
41ab1584 + InvertedIndices v1.0.0
82899510 + IteratorInterfaceExtensions v1.0.0
033835bb + JLD2 v0.1.12
682c06a0 + JSON v0.21.0
2ec943e9 + Libz v1.0.1
093fc24a + LightGraphs v1.3.1
259c3a9c + MMTF v0.1.0
1914dd2f + MacroTools v0.5.5
626554b9 + MetaGraphs v0.6.5
e1d29d7a + Missings v0.4.3
99f44e22 + MsgPack v0.2.0
bac558e1 + OrderedCollections v1.1.0
69de0a69 + Parsers v0.3.12
f27b6e38 + Polynomials v0.6.1
2dfb63ee + PooledArrays v0.5.3
3cdcf5f2 + RecipesBase v0.8.0
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 v1.0.3
3bb67fe8 + TranscodingStreams v0.9.5
7200193e + Twiddle v1.1.1
30578b45 + URIParser v0.4.0
ddb6d928 + YAML v0.4.0
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`
Testing BioStructures
Status `/tmp/jl_7s73Py/Project.toml`
00701ae9 BioAlignments v1.0.1
37cfa864 BioCore v2.0.5
7e6ae17a BioSequences v1.1.0
de9282ab BioStructures v0.9.3
3c28c6f8 BioSymbols v3.1.0
944b1d66 CodecZlib v0.6.0
a93c6f00 DataFrames v0.20.2
1fa38f19 Format v1.1.0
093fc24a LightGraphs v1.3.1
259c3a9c MMTF v0.1.0
626554b9 MetaGraphs v0.6.5
3cdcf5f2 RecipesBase v0.8.0
37e2e46d LinearAlgebra
10745b16 Statistics
8dfed614 Test
Status `/tmp/jl_7s73Py/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 v0.9.3
3c28c6f8 BioSymbols v3.1.0
e1450e63 BufferedStreams v1.0.0
324d7699 CategoricalArrays v0.7.7
944b1d66 CodecZlib v0.6.0
3da002f7 ColorTypes v0.9.1
861a8166 Combinatorics v0.7.0
34da2185 Compat v2.2.0
9a962f9c DataAPI v1.1.0
a93c6f00 DataFrames v0.20.2
864edb3b DataStructures v0.17.10
e2d170a0 DataValueInterfaces v1.0.0
5789e2e9 FileIO v1.2.4
53c48c17 FixedPointNumbers v0.7.1
1fa38f19 Format v1.1.0
899a7d2d GenomicFeatures v1.0.4
1cb3b9ac IndexableBitVectors v1.0.0
d25df0c9 Inflate v0.1.2
524e6230 IntervalTrees v1.0.0
41ab1584 InvertedIndices v1.0.0
82899510 IteratorInterfaceExtensions v1.0.0
033835bb JLD2 v0.1.12
682c06a0 JSON v0.21.0
2ec943e9 Libz v1.0.1
093fc24a LightGraphs v1.3.1
259c3a9c MMTF v0.1.0
1914dd2f MacroTools v0.5.5
626554b9 MetaGraphs v0.6.5
e1d29d7a Missings v0.4.3
99f44e22 MsgPack v0.2.0
bac558e1 OrderedCollections v1.1.0
69de0a69 Parsers v0.3.12
f27b6e38 Polynomials v0.6.1
2dfb63ee PooledArrays v0.5.3
3cdcf5f2 RecipesBase v0.8.0
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 v1.0.3
3bb67fe8 TranscodingStreams v0.9.5
7200193e Twiddle v1.1.1
30578b45 URIParser v0.4.0
ddb6d928 YAML v0.4.0
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
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 | 334 334
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