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1.5.0-DEV-e0740fe5a6.log
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Julia Version 1.5.0-DEV.147
Commit e0740fe5a6 (2020-01-24 14:13 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 Requires ─────────────── v1.0.0
Installed PositiveFactorizations ─ v0.2.3
Installed Missings ─────────────── v0.4.3
Installed Compat ───────────────── v2.2.0
Installed ASE ──────────────────── v0.5.1
Installed ArrayInterface ───────── v2.3.1
Installed OrderedCollections ───── v1.1.0
Installed StatsBase ────────────── v0.32.0
Installed OpenSpecFun_jll ──────── v0.5.3+1
Installed AlgebraicMultigrid ───── v0.2.2
Installed RecipesBase ──────────── v0.7.0
Installed NLSolversBase ────────── v7.6.0
Installed PyCall ───────────────── v1.91.2
Installed NeighbourLists ───────── v0.5.0
Installed IterativeSolvers ─────── v0.8.1
Installed Optim ────────────────── v0.20.0
Installed Reexport ─────────────── v0.2.0
Installed Conda ────────────────── v1.3.0
Installed FillArrays ───────────── v0.8.4
Installed FiniteDiff ───────────── v2.0.0
Installed JSON ─────────────────── v0.21.0
Installed CommonSubexpressions ─── v0.2.0
Installed NaNMath ──────────────── v0.3.3
Installed JuLIP ────────────────── v0.8.2
Installed DataAPI ──────────────── v1.1.0
Installed FunctionWrappers ─────── v1.0.0
Installed MacroTools ───────────── v0.5.3
Installed StaticArrays ─────────── v0.12.1
Installed SpecialFunctions ─────── v0.9.0
Installed DataStructures ───────── v0.17.9
Installed DiffRules ────────────── v1.0.0
Installed ForwardDiff ──────────── v0.10.9
Installed Dierckx ──────────────── v0.4.1
Installed Calculus ─────────────── v0.5.1
Installed VersionParsing ───────── v1.2.0
Installed Parsers ──────────────── v0.3.10
Installed Parameters ───────────── v0.12.0
Installed BinaryProvider ───────── v0.5.8
Installed DiffResults ──────────── v1.0.2
Installed SortingAlgorithms ────── v0.3.1
Installed LineSearches ─────────── v7.0.1
Updating `~/.julia/environments/v1.5/Project.toml`
[51974c44] + ASE v0.5.1
Updating `~/.julia/environments/v1.5/Manifest.toml`
[51974c44] + ASE v0.5.1
[2169fc97] + AlgebraicMultigrid v0.2.2
[4fba245c] + ArrayInterface v2.3.1
[b99e7846] + BinaryProvider v0.5.8
[49dc2e85] + Calculus v0.5.1
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v2.2.0
[8f4d0f93] + Conda v1.3.0
[9a962f9c] + DataAPI v1.1.0
[864edb3b] + DataStructures v0.17.9
[39dd38d3] + Dierckx v0.4.1
[163ba53b] + DiffResults v1.0.2
[b552c78f] + DiffRules v1.0.0
[1a297f60] + FillArrays v0.8.4
[6a86dc24] + FiniteDiff v2.0.0
[f6369f11] + ForwardDiff v0.10.9
[069b7b12] + FunctionWrappers v1.0.0
[42fd0dbc] + IterativeSolvers v0.8.1
[682c06a0] + JSON v0.21.0
[945c410c] + JuLIP v0.8.2
[d3d80556] + LineSearches v7.0.1
[1914dd2f] + MacroTools v0.5.3
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.6.0
[77ba4419] + NaNMath v0.3.3
[2fcf5ba9] + NeighbourLists v0.5.0
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.20.0
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[85a6dd25] + PositiveFactorizations v0.2.3
[438e738f] + PyCall v1.91.2
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[81def892] + VersionParsing v1.2.0
[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
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Dierckx → `~/.julia/packages/Dierckx/9SY4A/deps/build.log`
Updating `/tmp/jl_eCUX3k/Project.toml`
[no changes]
Updating `/tmp/jl_eCUX3k/Manifest.toml`
[no changes]
Building Conda ──→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Updating `/tmp/jl_JGXwhq/Project.toml`
[no changes]
Updating `/tmp/jl_JGXwhq/Manifest.toml`
[no changes]
Building PyCall ─→ `~/.julia/packages/PyCall/ttONZ/deps/build.log`
Updating `/tmp/jl_sCvWIx/Project.toml`
[no changes]
Updating `/tmp/jl_sCvWIx/Manifest.toml`
[no changes]
Building ASE ────→ `~/.julia/packages/ASE/GfCjR/deps/build.log`
Updating `/tmp/jl_1EbXo9/Project.toml`
[no changes]
Updating `/tmp/jl_1EbXo9/Manifest.toml`
[no changes]
┌ Error: Error building `ASE`:
│ /usr/bin/python3: No module named pip
│ WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
│ Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
│ To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
│ Collecting pip
│ Downloading pip-20.0.2-py2.py3-none-any.whl (1.4 MB)
│ Collecting setuptools
│ Downloading setuptools-45.1.0-py3-none-any.whl (583 kB)
│ Collecting wheel
│ Downloading wheel-0.33.6-py2.py3-none-any.whl (21 kB)
│ Installing collected packages: pip, setuptools, wheel
│ WARNING: The scripts pip, pip3 and pip3.6 are installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ WARNING: The scripts easy_install and easy_install-3.6 are installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ WARNING: The script wheel is installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ Successfully installed pip-20.0.2 setuptools-45.1.0 wheel-0.33.6
│ Collecting ase
│ Downloading ase-3.19.0-py3-none-any.whl (2.1 MB)
│ Requirement already satisfied, skipping upgrade: matplotlib in /usr/lib/python3/dist-packages (from ase) (2.1.1)
│ Collecting scipy
│ Downloading scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
│ Requirement already satisfied, skipping upgrade: numpy in /usr/lib/python3/dist-packages (from ase) (1.13.3)
│ Installing collected packages: scipy, ase
│ WARNING: The scripts ase, ase-build, ase-db, ase-gui, ase-info and ase-run are installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ Successfully installed ase-3.19.0 scipy-1.4.1
│ pip 20.0.2 from /home/pkgeval/.local/lib/python3.6/site-packages/pip (python 3.6)
│ Collecting matscipy
│ Downloading matscipy-0.3.0.tar.gz (154 kB)
│ Building wheels for collected packages: matscipy
│ Building wheel for matscipy (setup.py): started
│ Building wheel for matscipy (setup.py): finished with status 'error'
│ ERROR: Command errored out with exit status 1:
│ command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1j0ru3xg/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1j0ru3xg/matscipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-s2h3j_7z
│ cwd: /tmp/pip-install-1j0ru3xg/matscipy/
│ Complete output (107 lines):
│ running bdist_wheel
│ running build
│ running config_cc
│ unifing config_cc, config, build_clib, build_ext, build commands --compiler options
│ running config_fc
│ unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
│ running build_src
│ build_src
│ building extension "_matscipy" sources
│ build_src: building npy-pkg config files
│ running build_py
│ creating build
│ creating build/lib.linux-x86_64-3.6
│ creating build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/spatial_correlation_function.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/_version.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/atomic_strain.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/opls.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/drift.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/__init__.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/socketcalc.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/logger.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/deformation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/angle_distribution.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/dislocation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/neighbours.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/visualise.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/rings.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/elasticity.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/distributed_computation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/hydrogenate.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/surface.py -> build/lib.linux-x86_64-3.6/matscipy
│ creating build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/clusters.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/energy_release.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crackpathsel.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crack.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/idealbrittlesolid.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/Hertz.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/analysis.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/greens_function.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/DMT.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/JKR.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/supercell_calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/fitting.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/io.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ creating build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/opls.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/tbl.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/metis.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ creating build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/plot.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/qm_cluster.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/cluster_data.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_control.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_worker.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_mcfm.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_base.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/base_qm_cluster_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_clustering_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_flagging_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ UPDATING build/lib.linux-x86_64-3.6/matscipy/_version.py
│ set build/lib.linux-x86_64-3.6/matscipy/_version.py to '0.3.0'
│ running build_ext
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ building '_matscipy' extension
│ compiling C sources with arguments []
│ C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
│
│ creating build/temp.linux-x86_64-3.6
│ creating build/temp.linux-x86_64-3.6/c
│ compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c c/tools.c -o build/temp.linux-x86_64-3.6/c/tools.o -MMD -MF build/temp.linux-x86_64-3.6/c/tools.o.d" failed with exit status 1
│ ----------------------------------------
│ ERROR: Failed building wheel for matscipy
│ Running setup.py clean for matscipy
│ Failed to build matscipy
│ Installing collected packages: matscipy
│ Running setup.py install for matscipy: started
│ Running setup.py install for matscipy: finished with status 'error'
│ ERROR: Command errored out with exit status 1:
│ command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1j0ru3xg/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1j0ru3xg/matscipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-kpd88rqy/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/pkgeval/.local/include/python3.6m/matscipy
│ cwd: /tmp/pip-install-1j0ru3xg/matscipy/
│ Complete output (107 lines):
│ running install
│ running build
│ running config_cc
│ unifing config_cc, config, build_clib, build_ext, build commands --compiler options
│ running config_fc
│ unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
│ running build_src
│ build_src
│ building extension "_matscipy" sources
│ build_src: building npy-pkg config files
│ running build_py
│ creating build
│ creating build/lib.linux-x86_64-3.6
│ creating build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/spatial_correlation_function.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/_version.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/atomic_strain.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/opls.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/drift.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/__init__.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/socketcalc.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/logger.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/deformation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/angle_distribution.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/dislocation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/neighbours.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/visualise.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/rings.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/elasticity.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/distributed_computation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/hydrogenate.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/surface.py -> build/lib.linux-x86_64-3.6/matscipy
│ creating build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/clusters.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/energy_release.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crackpathsel.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crack.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/idealbrittlesolid.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/Hertz.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/analysis.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/greens_function.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/DMT.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/JKR.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/supercell_calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/fitting.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/io.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ creating build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/opls.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/tbl.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/metis.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ creating build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/plot.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/qm_cluster.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/cluster_data.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_control.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_worker.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_mcfm.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_base.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/base_qm_cluster_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_clustering_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_flagging_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ UPDATING build/lib.linux-x86_64-3.6/matscipy/_version.py
│ set build/lib.linux-x86_64-3.6/matscipy/_version.py to '0.3.0'
│ running build_ext
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ building '_matscipy' extension
│ compiling C sources with arguments []
│ C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
│
│ creating build/temp.linux-x86_64-3.6
│ creating build/temp.linux-x86_64-3.6/c
│ compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c c/tools.c -o build/temp.linux-x86_64-3.6/c/tools.o -MMD -MF build/temp.linux-x86_64-3.6/c/tools.o.d" failed with exit status 1
│ ----------------------------------------
│ ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1j0ru3xg/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1j0ru3xg/matscipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-kpd88rqy/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/pkgeval/.local/include/python3.6m/matscipy Check the logs for full command output.
│ ERROR: LoadError: failed process: Process(`python3 -m pip install --upgrade --user matscipy`, ProcessExited(1)) [1]
│
│ Stacktrace:
│ [1] pipeline_error at ./process.jl:525 [inlined]
│ [2] run(::Cmd; wait::Bool) at ./process.jl:440
│ [3] run at ./process.jl:438 [inlined]
│ [4] pip(::String) at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:22
│ [5] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:44
│ [6] include(::String) at ./client.jl:439
│ [7] top-level scope at none:5
│ in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:28
│ caused by [exception 1]
│ PyError (PyImport_ImportModule
│
│ The Python package matscipy could not be found by pyimport. Usually this means
│ that you did not install matscipy in the Python version being used by PyCall.
│
│ PyCall is currently configured to use the Python version at:
│
│ /usr/bin/python3
│
│ and you should use whatever mechanism you usually use (apt-get, pip, conda,
│ etcetera) to install the Python package containing the matscipy module.
│
│ One alternative is to re-configure PyCall to use a different Python
│ version on your system: set ENV["PYTHON"] to the path/name of the python
│ executable you want to use, run Pkg.build("PyCall"), and re-launch Julia.
│
│ Another alternative is to configure PyCall to use a Julia-specific Python
│ distribution via the Conda.jl package (which installs a private Anaconda
│ Python distribution), which has the advantage that packages can be installed
│ and kept up-to-date via Julia. As explained in the PyCall documentation,
│ set ENV["PYTHON"]="", run Pkg.build("PyCall"), and re-launch Julia. Then,
│ To install the matscipy module, you can use `pyimport_conda("matscipy", PKG)`,
│ where PKG is the Anaconda package the contains the module matscipy,
│ or alternatively you can use the Conda package directly (via
│ `using Conda` followed by `Conda.add` etcetera).
│
│ ) <class 'ModuleNotFoundError'>
│ ModuleNotFoundError("No module named 'matscipy'",)
│
│ Stacktrace:
│ [1] pyimport(::String) at /home/pkgeval/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
│ [2] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:39
│ [3] include(::String) at ./client.jl:439
│ [4] top-level scope at none:5
│ Installing Dependencies of `ASE.jl`: `ase` and `matscipy`
│ `ase` was not found, trying to install via pip. If this fails,
│ please file an issue and try to install it manually, following
│ the instructions at `https://wiki.fysik.dtu.dk/ase/install.html`
│ I couldn't find `pip`. I will try to download and install it
│ automatically, but if this fails, please install
│ manually, then try to build `ASE` again.
│ `matscipy` was not found, trying to install it. If this fails,
│ please file an issue and try to install it manually, following
│ the instructions at `https://github.com/libAtoms/matscipy`
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:883
Testing ASE
Updating `/tmp/jl_eTIgAs/Project.toml`
[no changes]
Updating `/tmp/jl_eTIgAs/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_eTIgAs/Project.toml`
[51974c44] ASE v0.5.1
[945c410c] JuLIP v0.8.2
[2fcf5ba9] NeighbourLists v0.5.0
[d96e819e] Parameters v0.12.0
[438e738f] PyCall v1.91.2
[189a3867] Reexport v0.2.0
[37e2e46d] LinearAlgebra
[8dfed614] Test
ERROR: LoadError: LoadError: LoadError: LoadError: PyError (PyImport_ImportModule
The Python package matscipy.neighbours could not be found by pyimport. Usually this means
that you did not install matscipy.neighbours in the Python version being used by PyCall.
PyCall is currently configured to use the Python version at:
/usr/bin/python3
and you should use whatever mechanism you usually use (apt-get, pip, conda,
etcetera) to install the Python package containing the matscipy.neighbours module.
One alternative is to re-configure PyCall to use a different Python
version on your system: set ENV["PYTHON"] to the path/name of the python
executable you want to use, run Pkg.build("PyCall"), and re-launch Julia.
Another alternative is to configure PyCall to use a Julia-specific Python
distribution via the Conda.jl package (which installs a private Anaconda
Python distribution), which has the advantage that packages can be installed
and kept up-to-date via Julia. As explained in the PyCall documentation,
set ENV["PYTHON"]="", run Pkg.build("PyCall"), and re-launch Julia. Then,
To install the matscipy.neighbours module, you can use `pyimport_conda("matscipy.neighbours", PKG)`,
where PKG is the Anaconda package the contains the module matscipy.neighbours,
or alternatively you can use the Conda package directly (via
`using Conda` followed by `Conda.add` etcetera).
) <class 'ModuleNotFoundError'>
ModuleNotFoundError("No module named 'matscipy'",)
Stacktrace:
[1] pyimport(::String) at /home/pkgeval/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
[2] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
[3] include(::Module, ::String) at ./Base.jl:377
[4] include(::String) at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[5] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/src/nlist.jl:7
[6] include(::Module, ::String) at ./Base.jl:377
[7] include(::String) at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[8] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:355
[9] include(::Module, ::String) at ./Base.jl:377
[10] _require(::Base.PkgId) at ./loading.jl:1058
[11] require(::Base.PkgId) at ./loading.jl:927
[12] require(::Module, ::Symbol) at ./loading.jl:922
[13] include(::String) at ./client.jl:439
[14] top-level scope at none:6
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/src/nlist.jl:7
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:355
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/test/runtests.jl:2
err = ProcessFailedException(Base.Process[Process(`/opt/julia/bin/julia -Cnative -J/opt/julia/lib/julia/sys.so -g1 --code-coverage=none --color=no --compiled-modules=yes --check-bounds=yes --inline=yes --startup-file=no --track-allocation=none --eval 'append!(empty!(Base.DEPOT_PATH), ["/home/pkgeval/.julia", "/opt/julia/local/share/julia", "/opt/julia/share/julia", "/usr/local/share/julia"])
append!(empty!(Base.DL_LOAD_PATH), String[])
cd("/home/pkgeval/.julia/packages/ASE/GfCjR/test")
append!(empty!(ARGS), String[])
include("/home/pkgeval/.julia/packages/ASE/GfCjR/test/runtests.jl")
'`, ProcessExited(1))])
ERROR: Package ASE errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:54
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1471
[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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:313
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:300
[5] #test#66 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
[6] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
[7] #test#65 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
[8] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
[10] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
[11] top-level scope at none:13