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Results with Julia v1.2.0
Testing was unsuccessful : testing failed for unknown reasons.
Last evaluation was ago and took 5 minutes, 6 seconds.
Click here to download the log file.
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Resolving package versions...
Installed DataAPI ──────────────── v1.1.0
Installed Missings ─────────────── v0.4.3
Installed ASE ──────────────────── v0.5.1
Installed CommonSubexpressions ─── v0.2.0
Installed LineSearches ─────────── v7.0.1
Installed BinaryProvider ───────── v0.5.8
Installed StatsBase ────────────── v0.32.0
Installed JuLIP ────────────────── v0.8.2
Installed AlgebraicMultigrid ───── v0.2.2
Installed URIParser ────────────── v0.4.0
Installed Reexport ─────────────── v0.2.0
Installed Requires ─────────────── v0.5.2
Installed Conda ────────────────── v1.3.0
Installed NLSolversBase ────────── v7.5.0
Installed NeighbourLists ───────── v0.5.0
Installed PyCall ───────────────── v1.91.2
Installed Compat ───────────────── v2.2.0
Installed FunctionWrappers ─────── v1.0.0
Installed Calculus ─────────────── v0.5.1
Installed OrderedCollections ───── v1.1.0
Installed ForwardDiff ──────────── v0.10.7
Installed IterativeSolvers ─────── v0.8.1
Installed Parsers ──────────────── v0.3.10
Installed RecipesBase ──────────── v0.7.0
Installed DataStructures ───────── v0.17.6
Installed FillArrays ───────────── v0.8.2
Installed DiffRules ────────────── v0.1.0
Installed JSON ─────────────────── v0.21.0
Installed ArrayInterface ───────── v2.0.0
Installed DiffEqDiffTools ──────── v1.5.0
Installed StaticArrays ─────────── v0.12.1
Installed NaNMath ──────────────── v0.3.3
Installed DiffResults ──────────── v0.0.4
Installed Parameters ───────────── v0.12.0
Installed SortingAlgorithms ────── v0.3.1
Installed Dierckx ──────────────── v0.4.1
Installed VersionParsing ───────── v1.1.3
Installed MacroTools ───────────── v0.5.2
Installed SpecialFunctions ─────── v0.8.0
Installed PositiveFactorizations ─ v0.2.3
Installed BinDeps ──────────────── v0.8.10
Installed Optim ────────────────── v0.19.5
Updating `~/.julia/environments/v1.2/Project.toml`
[51974c44] + ASE v0.5.1
Updating `~/.julia/environments/v1.2/Manifest.toml`
[51974c44] + ASE v0.5.1
[2169fc97] + AlgebraicMultigrid v0.2.2
[4fba245c] + ArrayInterface v2.0.0
[9e28174c] + BinDeps v0.8.10
[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 v0.17.6
[39dd38d3] + Dierckx v0.4.1
[01453d9d] + DiffEqDiffTools v1.5.0
[163ba53b] + DiffResults v0.0.4
[b552c78f] + DiffRules v0.1.0
[1a297f60] + FillArrays v0.8.2
[f6369f11] + ForwardDiff v0.10.7
[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 v0.5.2
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[2fcf5ba9] + NeighbourLists v0.5.0
[429524aa] + Optim v0.19.5
[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 v0.5.2
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[30578b45] + URIParser v0.4.0
[81def892] + VersionParsing v1.1.3
[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 SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
Building Dierckx ─────────→ `~/.julia/packages/Dierckx/9SY4A/deps/build.log`
Building Conda ───────────→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Building PyCall ──────────→ `~/.julia/packages/PyCall/ttONZ/deps/build.log`
Building ASE ─────────────→ `~/.julia/packages/ASE/GfCjR/deps/build.log`
┌ Error: Error building `ASE`:
│ /usr/bin/python3: No module named pip
│ Collecting pip
│ Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB)
│ Collecting setuptools
│ Downloading https://files.pythonhosted.org/packages/54/28/c45d8b54c1339f9644b87663945e54a8503cfef59cf0f65b3ff5dd17cf64/setuptools-42.0.2-py2.py3-none-any.whl (583kB)
│ Collecting wheel
│ Downloading https://files.pythonhosted.org/packages/00/83/b4a77d044e78ad1a45610eb88f745be2fd2c6d658f9798a15e384b7d57c9/wheel-0.33.6-py2.py3-none-any.whl
│ Installing collected packages: pip, setuptools, wheel
│ WARNING: The scripts pip, pip3 and pip3.6 are installed in '/root/.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 '/root/.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 '/root/.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-19.3.1 setuptools-42.0.2 wheel-0.33.6
│ Collecting ase
│ Downloading https://files.pythonhosted.org/packages/fc/cb/314601dc48d55c7c9c4f481f3099669c0f496da7c9fdddecfe74b2fdc6b2/ase-3.18.1-py3-none-any.whl (2.0MB)
│ Collecting scipy
│ Downloading https://files.pythonhosted.org/packages/54/18/d7c101d5e93b6c78dc206fcdf7bd04c1f8138a7b1a93578158fa3b132b08/scipy-1.3.3-cp36-cp36m-manylinux1_x86_64.whl (25.2MB)
│ Collecting numpy
│ Downloading https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0MB)
│ Collecting matplotlib
│ Downloading https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1MB)
│ Collecting kiwisolver>=1.0.1
│ Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB)
│ Collecting cycler>=0.10
│ Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
│ Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
│ Downloading https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl (67kB)
│ Collecting python-dateutil>=2.1
│ Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
│ Requirement already satisfied, skipping upgrade: setuptools in /root/.local/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->ase) (42.0.2)
│ Collecting six
│ Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
│ Installing collected packages: numpy, scipy, kiwisolver, six, cycler, pyparsing, python-dateutil, matplotlib, ase
│ WARNING: The scripts f2py, f2py3 and f2py3.6 are installed in '/root/.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 ase, ase-build, ase-db, ase-gui, ase-info and ase-run are installed in '/root/.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-3.18.1 cycler-0.10.0 kiwisolver-1.1.0 matplotlib-3.1.2 numpy-1.17.4 pyparsing-2.4.5 python-dateutil-2.8.1 scipy-1.3.3 six-1.13.0
│ pip 19.3.1 from /root/.local/lib/python3.6/site-packages/pip (python 3.6)
│ Collecting matscipy
│ Downloading https://files.pythonhosted.org/packages/df/28/f8c5f4d64d96fa6717f258e389639ed24649ead9198ab4ac60368785ba31/matscipy-0.3.0.tar.gz (154kB)
│ 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-1l5upv2v/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1l5upv2v/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-tizom0oh --python-tag cp36
│ cwd: /tmp/pip-install-1l5upv2v/matscipy/
│ Complete output (117 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/c
│ compile options: '-I/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ x86_64-linux-gnu-gcc: c/angle_distribution.c
│ x86_64-linux-gnu-gcc: c/neighbours.c
│ x86_64-linux-gnu-gcc: c/matscipymodule.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/neighbours.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/angle_distribution.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/matscipymodule.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/root/.local/lib/python3.6/site-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-1l5upv2v/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1l5upv2v/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-o9ksvl0k/install-record.txt --single-version-externally-managed --compile --user --prefix=
│ cwd: /tmp/pip-install-1l5upv2v/matscipy/
│ Complete output (117 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/c
│ compile options: '-I/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ x86_64-linux-gnu-gcc: c/angle_distribution.c
│ x86_64-linux-gnu-gcc: c/neighbours.c
│ x86_64-linux-gnu-gcc: c/matscipymodule.c
│ c/angle_distribution.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/neighbours.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.
│ c/matscipymodule.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/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c c/angle_distribution.c -o build/temp.linux-x86_64-3.6/c/angle_distribution.o -MMD -MF build/temp.linux-x86_64-3.6/c/angle_distribution.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-1l5upv2v/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1l5upv2v/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-o9ksvl0k/install-record.txt --single-version-externally-managed --compile --user --prefix= 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:813 [inlined]
│ [2] #run#536(::Bool, ::typeof(run), ::Cmd) at ./process.jl:728
│ [3] run at ./process.jl:726 [inlined]
│ [4] pip(::String) at /root/.julia/packages/ASE/GfCjR/deps/build.jl:22
│ [5] top-level scope at /root/.julia/packages/ASE/GfCjR/deps/build.jl:44
│ [6] include at ./boot.jl:328 [inlined]
│ [7] include_relative(::Module, ::String) at ./loading.jl:1094
│ [8] include(::Module, ::String) at ./Base.jl:31
│ [9] include(::String) at ./client.jl:431
│ [10] top-level scope at none:5
│ in expression starting at /root/.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 /root/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
│ [2] top-level scope at /root/.julia/packages/ASE/GfCjR/deps/build.jl:39
│ [3] include at ./boot.jl:328 [inlined]
│ [4] include_relative(::Module, ::String) at ./loading.jl:1094
│ [5] include(::Module, ::String) at ./Base.jl:31
│ [6] include(::String) at ./client.jl:431
│ [7] 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/v1.2/Pkg/src/backwards_compatible_isolation.jl:647
Testing ASE
Resolving package versions...
Status `/tmp/jl_dIo2Qn/Manifest.toml`
[51974c44] ASE v0.5.1
[2169fc97] AlgebraicMultigrid v0.2.2
[4fba245c] ArrayInterface v2.0.0
[9e28174c] BinDeps v0.8.10
[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 v0.17.6
[39dd38d3] Dierckx v0.4.1
[01453d9d] DiffEqDiffTools v1.5.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.1.0
[1a297f60] FillArrays v0.8.2
[f6369f11] ForwardDiff v0.10.7
[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 v0.5.2
[e1d29d7a] Missings v0.4.3
[d41bc354] NLSolversBase v7.5.0
[77ba4419] NaNMath v0.3.3
[2fcf5ba9] NeighbourLists v0.5.0
[429524aa] Optim v0.19.5
[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 v0.5.2
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.8.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[30578b45] URIParser v0.4.0
[81def892] VersionParsing v1.1.3
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
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 /root/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
[2] top-level scope at /root/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1094
[5] include at ./Base.jl:31 [inlined]
[6] include(::String) at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[7] top-level scope at /root/.julia/packages/ASE/GfCjR/src/nlist.jl:7
[8] include at ./boot.jl:328 [inlined]
[9] include_relative(::Module, ::String) at ./loading.jl:1094
[10] include at ./Base.jl:31 [inlined]
[11] include(::String) at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[12] top-level scope at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:355
[13] include at ./boot.jl:328 [inlined]
[14] include_relative(::Module, ::String) at ./loading.jl:1094
[15] _require(::Base.PkgId) at ./loading.jl:1042
[16] require(::Base.PkgId) at ./loading.jl:911
[17] require(::Module, ::Symbol) at ./loading.jl:906
[18] include at ./boot.jl:328 [inlined]
[19] include_relative(::Module, ::String) at ./loading.jl:1094
[20] include(::Module, ::String) at ./Base.jl:31
[21] include(::String) at ./client.jl:431
[22] top-level scope at none:5
in expression starting at /root/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
in expression starting at /root/.julia/packages/ASE/GfCjR/src/nlist.jl:7
in expression starting at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:355
in expression starting at /root/.julia/packages/ASE/GfCjR/test/runtests.jl:2
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/v1.2/Pkg/src/Types.jl:112
[2] #test#119(::Bool, ::Nothing, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Operations.jl:1288
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:245
[5] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:233 [inlined]
[6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
[7] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
[8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
[9] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
[11] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
[12] top-level scope at none:10
Results with Julia v1.3.0
Testing was unsuccessful : testing failed for unknown reasons.
Last evaluation was ago and took 5 minutes, 14 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed SortingAlgorithms ────── v0.3.1
Installed NeighbourLists ───────── v0.5.0
Installed Dierckx ──────────────── v0.4.1
Installed ASE ──────────────────── v0.5.1
Installed DiffResults ──────────── v0.0.4
Installed DataStructures ───────── v0.17.6
Installed StaticArrays ─────────── v0.12.1
Installed LineSearches ─────────── v7.0.1
Installed BinaryProvider ───────── v0.5.8
Installed Compat ───────────────── v2.2.0
Installed MacroTools ───────────── v0.5.2
Installed FunctionWrappers ─────── v1.0.0
Installed NLSolversBase ────────── v7.5.0
Installed Parsers ──────────────── v0.3.10
Installed Parameters ───────────── v0.12.0
Installed Missings ─────────────── v0.4.3
Installed PositiveFactorizations ─ v0.2.3
Installed OrderedCollections ───── v1.1.0
Installed PyCall ───────────────── v1.91.2
Installed CommonSubexpressions ─── v0.2.0
Installed JSON ─────────────────── v0.21.0
Installed SpecialFunctions ─────── v0.9.0
Installed RecipesBase ──────────── v0.7.0
Installed DataAPI ──────────────── v1.1.0
Installed ForwardDiff ──────────── v0.10.7
Installed NaNMath ──────────────── v0.3.3
Installed OpenSpecFun_jll ──────── v0.5.3+1
Installed DiffRules ────────────── v0.1.0
Installed Optim ────────────────── v0.19.5
Installed Conda ────────────────── v1.3.0
Installed DiffEqDiffTools ──────── v1.5.0
Installed Calculus ─────────────── v0.5.1
Installed ArrayInterface ───────── v2.0.0
Installed VersionParsing ───────── v1.1.3
Installed Reexport ─────────────── v0.2.0
Installed AlgebraicMultigrid ───── v0.2.2
Installed Requires ─────────────── v0.5.2
Installed StatsBase ────────────── v0.32.0
Installed FillArrays ───────────── v0.8.2
Installed JuLIP ────────────────── v0.8.2
Installed IterativeSolvers ─────── v0.8.1
Updating `~/.julia/environments/v1.3/Project.toml`
[51974c44] + ASE v0.5.1
Updating `~/.julia/environments/v1.3/Manifest.toml`
[51974c44] + ASE v0.5.1
[2169fc97] + AlgebraicMultigrid v0.2.2
[4fba245c] + ArrayInterface v2.0.0
[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 v0.17.6
[39dd38d3] + Dierckx v0.4.1
[01453d9d] + DiffEqDiffTools v1.5.0
[163ba53b] + DiffResults v0.0.4
[b552c78f] + DiffRules v0.1.0
[1a297f60] + FillArrays v0.8.2
[f6369f11] + ForwardDiff v0.10.7
[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 v0.5.2
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[2fcf5ba9] + NeighbourLists v0.5.0
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.19.5
[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 v0.5.2
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[81def892] + VersionParsing v1.1.3
[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`
Building Conda ──→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Building PyCall ─→ `~/.julia/packages/PyCall/ttONZ/deps/build.log`
Building ASE ────→ `~/.julia/packages/ASE/GfCjR/deps/build.log`
┌ Error: Error building `ASE`:
│ /usr/bin/python3: No module named pip
│ Collecting pip
│ Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB)
│ Collecting setuptools
│ Downloading https://files.pythonhosted.org/packages/54/28/c45d8b54c1339f9644b87663945e54a8503cfef59cf0f65b3ff5dd17cf64/setuptools-42.0.2-py2.py3-none-any.whl (583kB)
│ Collecting wheel
│ Downloading https://files.pythonhosted.org/packages/00/83/b4a77d044e78ad1a45610eb88f745be2fd2c6d658f9798a15e384b7d57c9/wheel-0.33.6-py2.py3-none-any.whl
│ Installing collected packages: pip, setuptools, wheel
│ WARNING: The scripts pip, pip3 and pip3.6 are installed in '/root/.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 '/root/.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 '/root/.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-19.3.1 setuptools-42.0.2 wheel-0.33.6
│ Collecting ase
│ Downloading https://files.pythonhosted.org/packages/fc/cb/314601dc48d55c7c9c4f481f3099669c0f496da7c9fdddecfe74b2fdc6b2/ase-3.18.1-py3-none-any.whl (2.0MB)
│ Collecting numpy
│ Downloading https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0MB)
│ Collecting matplotlib
│ Downloading https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1MB)
│ Collecting scipy
│ Downloading https://files.pythonhosted.org/packages/54/18/d7c101d5e93b6c78dc206fcdf7bd04c1f8138a7b1a93578158fa3b132b08/scipy-1.3.3-cp36-cp36m-manylinux1_x86_64.whl (25.2MB)
│ Collecting cycler>=0.10
│ Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
│ Collecting python-dateutil>=2.1
│ Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
│ Collecting kiwisolver>=1.0.1
│ Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB)
│ Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
│ Downloading https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl (67kB)
│ Collecting six
│ Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
│ Requirement already satisfied, skipping upgrade: setuptools in /root/.local/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->ase) (42.0.2)
│ Installing collected packages: numpy, six, cycler, python-dateutil, kiwisolver, pyparsing, matplotlib, scipy, ase
│ WARNING: The scripts f2py, f2py3 and f2py3.6 are installed in '/root/.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 ase, ase-build, ase-db, ase-gui, ase-info and ase-run are installed in '/root/.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-3.18.1 cycler-0.10.0 kiwisolver-1.1.0 matplotlib-3.1.2 numpy-1.17.4 pyparsing-2.4.5 python-dateutil-2.8.1 scipy-1.3.3 six-1.13.0
│ pip 19.3.1 from /root/.local/lib/python3.6/site-packages/pip (python 3.6)
│ Collecting matscipy
│ Downloading https://files.pythonhosted.org/packages/df/28/f8c5f4d64d96fa6717f258e389639ed24649ead9198ab4ac60368785ba31/matscipy-0.3.0.tar.gz (154kB)
│ 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-14cgjv5d/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-14cgjv5d/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-6ymed6c4 --python-tag cp36
│ cwd: /tmp/pip-install-14cgjv5d/matscipy/
│ Complete output (117 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/c
│ compile options: '-I/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ x86_64-linux-gnu-gcc: c/angle_distribution.c
│ x86_64-linux-gnu-gcc: c/neighbours.c
│ x86_64-linux-gnu-gcc: c/matscipymodule.c
│ c/matscipymodule.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ c/angle_distribution.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ compilation terminated.
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/neighbours.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/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c c/angle_distribution.c -o build/temp.linux-x86_64-3.6/c/angle_distribution.o -MMD -MF build/temp.linux-x86_64-3.6/c/angle_distribution.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-14cgjv5d/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-14cgjv5d/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-6ebz_ifh/install-record.txt --single-version-externally-managed --compile --user --prefix=
│ cwd: /tmp/pip-install-14cgjv5d/matscipy/
│ Complete output (117 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/c
│ compile options: '-I/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ x86_64-linux-gnu-gcc: c/angle_distribution.c
│ x86_64-linux-gnu-gcc: c/neighbours.c
│ x86_64-linux-gnu-gcc: c/matscipymodule.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/neighbours.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/angle_distribution.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/matscipymodule.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/root/.local/lib/python3.6/site-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-14cgjv5d/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-14cgjv5d/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-6ebz_ifh/install-record.txt --single-version-externally-managed --compile --user --prefix= 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#565(::Bool, ::typeof(run), ::Cmd) at ./process.jl:440
│ [3] run at ./process.jl:438 [inlined]
│ [4] pip(::String) at /root/.julia/packages/ASE/GfCjR/deps/build.jl:22
│ [5] top-level scope at /root/.julia/packages/ASE/GfCjR/deps/build.jl:44
│ [6] include at ./boot.jl:328 [inlined]
│ [7] include_relative(::Module, ::String) at ./loading.jl:1105
│ [8] include(::Module, ::String) at ./Base.jl:31
│ [9] include(::String) at ./client.jl:424
│ [10] top-level scope at none:5
│ in expression starting at /root/.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 /root/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
│ [2] top-level scope at /root/.julia/packages/ASE/GfCjR/deps/build.jl:39
│ [3] include at ./boot.jl:328 [inlined]
│ [4] include_relative(::Module, ::String) at ./loading.jl:1105
│ [5] include(::Module, ::String) at ./Base.jl:31
│ [6] include(::String) at ./client.jl:424
│ [7] 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/v1.3/Pkg/src/backwards_compatible_isolation.jl:649
Testing ASE
Resolving package versions...
Status `/tmp/jl_807fFK/Manifest.toml`
[51974c44] ASE v0.5.1
[2169fc97] AlgebraicMultigrid v0.2.2
[4fba245c] ArrayInterface v2.0.0
[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 v0.17.6
[39dd38d3] Dierckx v0.4.1
[01453d9d] DiffEqDiffTools v1.5.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.1.0
[1a297f60] FillArrays v0.8.2
[f6369f11] ForwardDiff v0.10.7
[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 v0.5.2
[e1d29d7a] Missings v0.4.3
[d41bc354] NLSolversBase v7.5.0
[77ba4419] NaNMath v0.3.3
[2fcf5ba9] NeighbourLists v0.5.0
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[429524aa] Optim v0.19.5
[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 v0.5.2
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[81def892] VersionParsing v1.1.3
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
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 /root/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
[2] top-level scope at /root/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1105
[5] include at ./Base.jl:31 [inlined]
[6] include(::String) at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[7] top-level scope at /root/.julia/packages/ASE/GfCjR/src/nlist.jl:7
[8] include at ./boot.jl:328 [inlined]
[9] include_relative(::Module, ::String) at ./loading.jl:1105
[10] include at ./Base.jl:31 [inlined]
[11] include(::String) at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[12] top-level scope at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:355
[13] include at ./boot.jl:328 [inlined]
[14] include_relative(::Module, ::String) at ./loading.jl:1105
[15] _require(::Base.PkgId) at ./loading.jl:1053
[16] require(::Base.PkgId) at ./loading.jl:922
[17] require(::Module, ::Symbol) at ./loading.jl:917
[18] include at ./boot.jl:328 [inlined]
[19] include_relative(::Module, ::String) at ./loading.jl:1105
[20] include(::Module, ::String) at ./Base.jl:31
[21] include(::String) at ./client.jl:424
[22] top-level scope at none:6
in expression starting at /root/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
in expression starting at /root/.julia/packages/ASE/GfCjR/src/nlist.jl:7
in expression starting at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:355
in expression starting at /root/.julia/packages/ASE/GfCjR/test/runtests.jl:2
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/v1.3/Pkg/src/Types.jl:113
[2] #test#131(::Bool, ::Nothing, ::Cmd, ::Cmd, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Operations.jl:1370
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Cmd, ::Cmd, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:253
[5] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:239
[6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[7] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[9] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[11] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[12] top-level scope at none:10
Results with Julia v1.3.1-pre-7704df0a5a
Testing was unsuccessful : testing failed for unknown reasons.
Last evaluation was ago and took 5 minutes, 24 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed FunctionWrappers ─────── v1.0.0
Installed OpenSpecFun_jll ──────── v0.5.3+1
Installed Conda ────────────────── v1.3.0
Installed ASE ──────────────────── v0.5.1
Installed PyCall ───────────────── v1.91.2
Installed DataStructures ───────── v0.17.6
Installed IterativeSolvers ─────── v0.8.1
Installed Optim ────────────────── v0.19.5
Installed SpecialFunctions ─────── v0.9.0
Installed Compat ───────────────── v2.2.0
Installed NaNMath ──────────────── v0.3.3
Installed AlgebraicMultigrid ───── v0.2.2
Installed StaticArrays ─────────── v0.12.1
Installed MacroTools ───────────── v0.5.2
Installed DiffResults ──────────── v0.0.4
Installed JuLIP ────────────────── v0.8.2
Installed FillArrays ───────────── v0.8.2
Installed StatsBase ────────────── v0.32.0
Installed ForwardDiff ──────────── v0.10.7
Installed Calculus ─────────────── v0.5.1
Installed CommonSubexpressions ─── v0.2.0
Installed LineSearches ─────────── v7.0.1
Installed Missings ─────────────── v0.4.3
Installed Dierckx ──────────────── v0.4.1
Installed NeighbourLists ───────── v0.5.0
Installed BinaryProvider ───────── v0.5.8
Installed Parameters ───────────── v0.12.0
Installed NLSolversBase ────────── v7.5.0
Installed Reexport ─────────────── v0.2.0
Installed Requires ─────────────── v0.5.2
Installed PositiveFactorizations ─ v0.2.3
Installed ArrayInterface ───────── v2.0.0
Installed RecipesBase ──────────── v0.7.0
Installed DataAPI ──────────────── v1.1.0
Installed DiffRules ────────────── v0.1.0
Installed JSON ─────────────────── v0.21.0
Installed DiffEqDiffTools ──────── v1.5.0
Installed VersionParsing ───────── v1.1.3
Installed OrderedCollections ───── v1.1.0
Installed Parsers ──────────────── v0.3.10
Installed SortingAlgorithms ────── v0.3.1
Updating `~/.julia/environments/v1.3/Project.toml`
[51974c44] + ASE v0.5.1
Updating `~/.julia/environments/v1.3/Manifest.toml`
[51974c44] + ASE v0.5.1
[2169fc97] + AlgebraicMultigrid v0.2.2
[4fba245c] + ArrayInterface v2.0.0
[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 v0.17.6
[39dd38d3] + Dierckx v0.4.1
[01453d9d] + DiffEqDiffTools v1.5.0
[163ba53b] + DiffResults v0.0.4
[b552c78f] + DiffRules v0.1.0
[1a297f60] + FillArrays v0.8.2
[f6369f11] + ForwardDiff v0.10.7
[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 v0.5.2
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[2fcf5ba9] + NeighbourLists v0.5.0
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.19.5
[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 v0.5.2
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[81def892] + VersionParsing v1.1.3
[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`
Building Conda ──→ `~/.julia/packages/Conda/kLXeC/deps/build.log`
Building PyCall ─→ `~/.julia/packages/PyCall/ttONZ/deps/build.log`
Building ASE ────→ `~/.julia/packages/ASE/GfCjR/deps/build.log`
┌ Error: Error building `ASE`:
│ /usr/bin/python3: No module named pip
│ Collecting pip
│ Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB)
│ Collecting setuptools
│ Downloading https://files.pythonhosted.org/packages/54/28/c45d8b54c1339f9644b87663945e54a8503cfef59cf0f65b3ff5dd17cf64/setuptools-42.0.2-py2.py3-none-any.whl (583kB)
│ Collecting wheel
│ Downloading https://files.pythonhosted.org/packages/00/83/b4a77d044e78ad1a45610eb88f745be2fd2c6d658f9798a15e384b7d57c9/wheel-0.33.6-py2.py3-none-any.whl
│ Installing collected packages: pip, setuptools, wheel
│ WARNING: The scripts pip, pip3 and pip3.6 are installed in '/root/.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 '/root/.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 '/root/.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-19.3.1 setuptools-42.0.2 wheel-0.33.6
│ Collecting ase
│ Downloading https://files.pythonhosted.org/packages/fc/cb/314601dc48d55c7c9c4f481f3099669c0f496da7c9fdddecfe74b2fdc6b2/ase-3.18.1-py3-none-any.whl (2.0MB)
│ Collecting matplotlib
│ Downloading https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1MB)
│ Collecting scipy
│ Downloading https://files.pythonhosted.org/packages/54/18/d7c101d5e93b6c78dc206fcdf7bd04c1f8138a7b1a93578158fa3b132b08/scipy-1.3.3-cp36-cp36m-manylinux1_x86_64.whl (25.2MB)
│ Collecting numpy
│ Downloading https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0MB)
│ Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
│ Downloading https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl (67kB)
│ Collecting kiwisolver>=1.0.1
│ Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB)
│ Collecting cycler>=0.10
│ Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
│ Collecting python-dateutil>=2.1
│ Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
│ Requirement already satisfied, skipping upgrade: setuptools in /root/.local/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->ase) (42.0.2)
│ Collecting six
│ Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
│ Installing collected packages: pyparsing, kiwisolver, numpy, six, cycler, python-dateutil, matplotlib, scipy, ase
│ WARNING: The scripts f2py, f2py3 and f2py3.6 are installed in '/root/.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 ase, ase-build, ase-db, ase-gui, ase-info and ase-run are installed in '/root/.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-3.18.1 cycler-0.10.0 kiwisolver-1.1.0 matplotlib-3.1.2 numpy-1.17.4 pyparsing-2.4.5 python-dateutil-2.8.1 scipy-1.3.3 six-1.13.0
│ pip 19.3.1 from /root/.local/lib/python3.6/site-packages/pip (python 3.6)
│ Collecting matscipy
│ Downloading https://files.pythonhosted.org/packages/df/28/f8c5f4d64d96fa6717f258e389639ed24649ead9198ab4ac60368785ba31/matscipy-0.3.0.tar.gz (154kB)
│ 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-4ej44doe/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4ej44doe/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-pdc4_75t --python-tag cp36
│ cwd: /tmp/pip-install-4ej44doe/matscipy/
│ Complete output (117 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/c
│ compile options: '-I/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/neighbours.c
│ x86_64-linux-gnu-gcc: c/tools.c
│ x86_64-linux-gnu-gcc: c/angle_distribution.c
│ x86_64-linux-gnu-gcc: c/matscipymodule.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ c/matscipymodule.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ compilation terminated.
│ c/angle_distribution.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ c/neighbours.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ 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/root/.local/lib/python3.6/site-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-4ej44doe/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4ej44doe/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-yk7cgl1d/install-record.txt --single-version-externally-managed --compile --user --prefix=
│ cwd: /tmp/pip-install-4ej44doe/matscipy/
│ Complete output (117 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/c
│ compile options: '-I/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ x86_64-linux-gnu-gcc: c/angle_distribution.c
│ x86_64-linux-gnu-gcc: c/matscipymodule.c
│ x86_64-linux-gnu-gcc: c/neighbours.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/angle_distribution.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/matscipymodule.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/neighbours.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/root/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c c/angle_distribution.c -o build/temp.linux-x86_64-3.6/c/angle_distribution.o -MMD -MF build/temp.linux-x86_64-3.6/c/angle_distribution.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-4ej44doe/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4ej44doe/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-yk7cgl1d/install-record.txt --single-version-externally-managed --compile --user --prefix= 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#565(::Bool, ::typeof(run), ::Cmd) at ./process.jl:440
│ [3] run at ./process.jl:438 [inlined]
│ [4] pip(::String) at /root/.julia/packages/ASE/GfCjR/deps/build.jl:22
│ [5] top-level scope at /root/.julia/packages/ASE/GfCjR/deps/build.jl:44
│ [6] include at ./boot.jl:328 [inlined]
│ [7] include_relative(::Module, ::String) at ./loading.jl:1105
│ [8] include(::Module, ::String) at ./Base.jl:31
│ [9] include(::String) at ./client.jl:424
│ [10] top-level scope at none:5
│ in expression starting at /root/.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 /root/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
│ [2] top-level scope at /root/.julia/packages/ASE/GfCjR/deps/build.jl:39
│ [3] include at ./boot.jl:328 [inlined]
│ [4] include_relative(::Module, ::String) at ./loading.jl:1105
│ [5] include(::Module, ::String) at ./Base.jl:31
│ [6] include(::String) at ./client.jl:424
│ [7] 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 /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649
Testing ASE
Resolving package versions...
Status `/tmp/jl_plMhnb/Manifest.toml`
[51974c44] ASE v0.5.1
[2169fc97] AlgebraicMultigrid v0.2.2
[4fba245c] ArrayInterface v2.0.0
[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 v0.17.6
[39dd38d3] Dierckx v0.4.1
[01453d9d] DiffEqDiffTools v1.5.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.1.0
[1a297f60] FillArrays v0.8.2
[f6369f11] ForwardDiff v0.10.7
[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 v0.5.2
[e1d29d7a] Missings v0.4.3
[d41bc354] NLSolversBase v7.5.0
[77ba4419] NaNMath v0.3.3
[2fcf5ba9] NeighbourLists v0.5.0
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[429524aa] Optim v0.19.5
[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 v0.5.2
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[81def892] VersionParsing v1.1.3
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
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 /root/.julia/packages/PyCall/ttONZ/src/PyCall.jl:544
[2] top-level scope at /root/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1105
[5] include at ./Base.jl:31 [inlined]
[6] include(::String) at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[7] top-level scope at /root/.julia/packages/ASE/GfCjR/src/nlist.jl:7
[8] include at ./boot.jl:328 [inlined]
[9] include_relative(::Module, ::String) at ./loading.jl:1105
[10] include at ./Base.jl:31 [inlined]
[11] include(::String) at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[12] top-level scope at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:355
[13] include at ./boot.jl:328 [inlined]
[14] include_relative(::Module, ::String) at ./loading.jl:1105
[15] _require(::Base.PkgId) at ./loading.jl:1053
[16] require(::Base.PkgId) at ./loading.jl:922
[17] require(::Module, ::Symbol) at ./loading.jl:917
[18] include at ./boot.jl:328 [inlined]
[19] include_relative(::Module, ::String) at ./loading.jl:1105
[20] include(::Module, ::String) at ./Base.jl:31
[21] include(::String) at ./client.jl:424
[22] top-level scope at none:6
in expression starting at /root/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
in expression starting at /root/.julia/packages/ASE/GfCjR/src/nlist.jl:7
in expression starting at /root/.julia/packages/ASE/GfCjR/src/ASE.jl:355
in expression starting at /root/.julia/packages/ASE/GfCjR/test/runtests.jl:2
ERROR: Package ASE errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:113
[2] #test#131(::Bool, ::Nothing, ::Cmd, ::Cmd, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/Operations.jl:1370
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Cmd, ::Cmd, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:253
[5] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:239
[6] #test#61 at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[7] test at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[8] #test#60 at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[9] test at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[11] test(::String) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[12] top-level scope at none:10