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1.5.0-DEV-7206b56e94.log
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Julia Version 1.5.0-DEV.485
Commit 7206b56e94 (2020-03-18 17:25 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed SortingAlgorithms ──────────── v0.3.1
Installed VersionParsing ─────────────── v1.2.0
Installed ASE ────────────────────────── v0.5.1
Installed FunctionWrappers ───────────── v1.1.1
Installed Parameters ─────────────────── v0.12.0
Installed Conda ──────────────────────── v1.4.1
Installed LineSearches ───────────────── v7.0.1
Installed StatsBase ──────────────────── v0.32.2
Installed CommonSubexpressions ───────── v0.2.0
Installed StaticArrays ───────────────── v0.12.1
Installed NaNMath ────────────────────── v0.3.3
Installed CompilerSupportLibraries_jll ─ v0.3.0+0
Installed Reexport ───────────────────── v0.2.0
Installed AlgebraicMultigrid ─────────── v0.2.2
Installed DiffResults ────────────────── v1.0.2
Installed JuLIP ──────────────────────── v0.8.2
Installed JSON ───────────────────────── v0.21.0
Installed DataStructures ─────────────── v0.17.10
Installed Optim ──────────────────────── v0.20.1
Installed RecipesBase ────────────────── v0.8.0
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed PositiveFactorizations ─────── v0.2.3
Installed Calculus ───────────────────── v0.5.1
Installed DataAPI ────────────────────── v1.1.0
Installed Parsers ────────────────────── v0.3.12
Installed SpecialFunctions ───────────── v0.10.0
Installed IterativeSolvers ───────────── v0.8.1
Installed Missings ───────────────────── v0.4.3
Installed Requires ───────────────────── v1.0.1
Installed FiniteDiff ─────────────────── v2.2.1
Installed BinaryProvider ─────────────── v0.5.8
Installed ArrayInterface ─────────────── v2.5.1
Installed NeighbourLists ─────────────── v0.5.0
Installed Dierckx ────────────────────── v0.4.1
Installed MacroTools ─────────────────── v0.5.4
Installed DiffRules ──────────────────── v1.0.1
Installed Compat ─────────────────────── v2.2.0
Installed ForwardDiff ────────────────── v0.10.9
Installed PyCall ─────────────────────── v1.91.4
Installed OrderedCollections ─────────── v1.1.0
Installed FillArrays ─────────────────── v0.8.5
Installed NLSolversBase ──────────────── v7.6.1
#=#=# ## 3.1%###### 8.6%########### 15.4%################# 24.6%########################## 36.7%#################################### 50.6%################################################ 66.8%############################################################### 87.8%######################################################################## 100.0%
#=#=# ######################################################################## 100.0%
Updating `~/.julia/environments/v1.5/Project.toml`
51974c44 + ASE v0.5.1
Updating `~/.julia/environments/v1.5/Manifest.toml`
51974c44 + ASE v0.5.1
2169fc97 + AlgebraicMultigrid v0.2.2
4fba245c + ArrayInterface v2.5.1
b99e7846 + BinaryProvider v0.5.8
49dc2e85 + Calculus v0.5.1
bbf7d656 + CommonSubexpressions v0.2.0
34da2185 + Compat v2.2.0
e66e0078 + CompilerSupportLibraries_jll v0.3.0+0
8f4d0f93 + Conda v1.4.1
9a962f9c + DataAPI v1.1.0
864edb3b + DataStructures v0.17.10
39dd38d3 + Dierckx v0.4.1
163ba53b + DiffResults v1.0.2
b552c78f + DiffRules v1.0.1
1a297f60 + FillArrays v0.8.5
6a86dc24 + FiniteDiff v2.2.1
f6369f11 + ForwardDiff v0.10.9
069b7b12 + FunctionWrappers v1.1.1
42fd0dbc + IterativeSolvers v0.8.1
682c06a0 + JSON v0.21.0
945c410c + JuLIP v0.8.2
d3d80556 + LineSearches v7.0.1
1914dd2f + MacroTools v0.5.4
e1d29d7a + Missings v0.4.3
d41bc354 + NLSolversBase v7.6.1
77ba4419 + NaNMath v0.3.3
2fcf5ba9 + NeighbourLists v0.5.0
efe28fd5 + OpenSpecFun_jll v0.5.3+3
429524aa + Optim v0.20.1
bac558e1 + OrderedCollections v1.1.0
d96e819e + Parameters v0.12.0
69de0a69 + Parsers v0.3.12
85a6dd25 + PositiveFactorizations v0.2.3
438e738f + PyCall v1.91.4
3cdcf5f2 + RecipesBase v0.8.0
189a3867 + Reexport v0.2.0
ae029012 + Requires v1.0.1
a2af1166 + SortingAlgorithms v0.3.1
276daf66 + SpecialFunctions v0.10.0
90137ffa + StaticArrays v0.12.1
2913bbd2 + StatsBase v0.32.2
81def892 + VersionParsing v1.2.0
2a0f44e3 + Base64
ade2ca70 + Dates
8bb1440f + DelimitedFiles
8ba89e20 + Distributed
b77e0a4c + InteractiveUtils
76f85450 + LibGit2
8f399da3 + Libdl
37e2e46d + LinearAlgebra
56ddb016 + Logging
d6f4376e + Markdown
a63ad114 + Mmap
44cfe95a + Pkg
de0858da + Printf
3fa0cd96 + REPL
9a3f8284 + Random
ea8e919c + SHA
9e88b42a + Serialization
1a1011a3 + SharedArrays
6462fe0b + Sockets
2f01184e + SparseArrays
10745b16 + Statistics
4607b0f0 + SuiteSparse
8dfed614 + Test
cf7118a7 + UUIDs
4ec0a83e + Unicode
Building Dierckx → `~/.julia/packages/Dierckx/9SY4A/deps/build.log`
Building Conda ──→ `~/.julia/packages/Conda/3rPhK/deps/build.log`
Building PyCall ─→ `~/.julia/packages/PyCall/zqDXB/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 pip-20.0.2-py2.py3-none-any.whl (1.4 MB)
│ Collecting setuptools
│ Downloading setuptools-46.0.0-py3-none-any.whl (582 kB)
│ Collecting wheel
│ Downloading wheel-0.34.2-py2.py3-none-any.whl (26 kB)
│ Installing collected packages: pip, setuptools, wheel
│ WARNING: The scripts pip, pip3 and pip3.6 are installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ WARNING: The scripts easy_install and easy_install-3.6 are installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ WARNING: The script wheel is installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ Successfully installed pip-20.0.2 setuptools-46.0.0 wheel-0.34.2
│ Collecting ase
│ Downloading ase-3.19.0-py3-none-any.whl (2.1 MB)
│ Collecting scipy
│ Downloading scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
│ Requirement already satisfied, skipping upgrade: matplotlib in /usr/lib/python3/dist-packages (from ase) (2.1.1)
│ Requirement already satisfied, skipping upgrade: numpy in /usr/lib/python3/dist-packages (from ase) (1.13.3)
│ Installing collected packages: scipy, ase
│ WARNING: The scripts ase, ase-build, ase-db, ase-gui, ase-info and ase-run are installed in '/home/pkgeval/.local/bin' which is not on PATH.
│ Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
│ Successfully installed ase-3.19.0 scipy-1.4.1
│ pip 20.0.2 from /home/pkgeval/.local/lib/python3.6/site-packages/pip (python 3.6)
│ Collecting matscipy
│ Downloading matscipy-0.3.0.tar.gz (154 kB)
│ Building wheels for collected packages: matscipy
│ Building wheel for matscipy (setup.py): started
│ Building wheel for matscipy (setup.py): finished with status 'error'
│ ERROR: Command errored out with exit status 1:
│ command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2za64ax3/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2za64ax3/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-8s9zdk2e
│ cwd: /tmp/pip-install-2za64ax3/matscipy/
│ Complete output (107 lines):
│ running bdist_wheel
│ running build
│ running config_cc
│ unifing config_cc, config, build_clib, build_ext, build commands --compiler options
│ running config_fc
│ unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
│ running build_src
│ build_src
│ building extension "_matscipy" sources
│ build_src: building npy-pkg config files
│ running build_py
│ creating build
│ creating build/lib.linux-x86_64-3.6
│ creating build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/spatial_correlation_function.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/_version.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/atomic_strain.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/opls.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/drift.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/__init__.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/socketcalc.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/logger.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/deformation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/angle_distribution.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/dislocation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/neighbours.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/visualise.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/rings.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/elasticity.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/distributed_computation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/hydrogenate.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/surface.py -> build/lib.linux-x86_64-3.6/matscipy
│ creating build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/clusters.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/energy_release.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crackpathsel.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crack.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/idealbrittlesolid.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/Hertz.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/analysis.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/greens_function.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/DMT.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/JKR.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/supercell_calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/fitting.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/io.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ creating build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/opls.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/tbl.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/metis.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ creating build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/plot.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/qm_cluster.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/cluster_data.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_control.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_worker.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_mcfm.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_base.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/base_qm_cluster_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_clustering_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_flagging_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ UPDATING build/lib.linux-x86_64-3.6/matscipy/_version.py
│ set build/lib.linux-x86_64-3.6/matscipy/_version.py to '0.3.0'
│ running build_ext
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ building '_matscipy' extension
│ compiling C sources with arguments []
│ C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
│
│ creating build/temp.linux-x86_64-3.6
│ creating build/temp.linux-x86_64-3.6/c
│ compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c c/tools.c -o build/temp.linux-x86_64-3.6/c/tools.o -MMD -MF build/temp.linux-x86_64-3.6/c/tools.o.d" failed with exit status 1
│ ----------------------------------------
│ ERROR: Failed building wheel for matscipy
│ Running setup.py clean for matscipy
│ Failed to build matscipy
│ Installing collected packages: matscipy
│ Running setup.py install for matscipy: started
│ Running setup.py install for matscipy: finished with status 'error'
│ ERROR: Command errored out with exit status 1:
│ command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2za64ax3/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2za64ax3/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-wjnbnlbz/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/pkgeval/.local/include/python3.6m/matscipy
│ cwd: /tmp/pip-install-2za64ax3/matscipy/
│ Complete output (107 lines):
│ running install
│ running build
│ running config_cc
│ unifing config_cc, config, build_clib, build_ext, build commands --compiler options
│ running config_fc
│ unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
│ running build_src
│ build_src
│ building extension "_matscipy" sources
│ build_src: building npy-pkg config files
│ running build_py
│ creating build
│ creating build/lib.linux-x86_64-3.6
│ creating build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/spatial_correlation_function.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/_version.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/atomic_strain.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/opls.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/drift.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/__init__.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/socketcalc.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/logger.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/deformation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/angle_distribution.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/dislocation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/neighbours.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/visualise.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/rings.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/elasticity.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/distributed_computation.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/hydrogenate.py -> build/lib.linux-x86_64-3.6/matscipy
│ copying matscipy/surface.py -> build/lib.linux-x86_64-3.6/matscipy
│ creating build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/clusters.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/energy_release.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crackpathsel.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/crack.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ copying matscipy/fracture_mechanics/idealbrittlesolid.py -> build/lib.linux-x86_64-3.6/matscipy/fracture_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/Hertz.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/analysis.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/greens_function.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/DMT.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ copying matscipy/contact_mechanics/JKR.py -> build/lib.linux-x86_64-3.6/matscipy/contact_mechanics
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/supercell_calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ copying matscipy/calculators/fitting.py -> build/lib.linux-x86_64-3.6/matscipy/calculators
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/io.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ copying matscipy/calculators/eam/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/eam
│ creating build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/opls.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/tbl.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ copying matscipy/io/metis.py -> build/lib.linux-x86_64-3.6/matscipy/io
│ creating build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/plot.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ copying matscipy/tool/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/tool
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ copying matscipy/calculators/pair_potential/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/pair_potential
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/qm_cluster.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/cluster_data.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ copying matscipy/calculators/mcfm/calculator.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_control.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ copying matscipy/calculators/mcfm/mcfm_parallel/mcfm_parallel_worker.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/mcfm_parallel
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_mcfm.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ copying matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_base.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/neighbour_list_mcfm
│ creating build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/base_qm_cluster_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/__init__.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_clustering_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ copying matscipy/calculators/mcfm/qm_cluster_tools/qm_flagging_tool.py -> build/lib.linux-x86_64-3.6/matscipy/calculators/mcfm/qm_cluster_tools
│ UPDATING build/lib.linux-x86_64-3.6/matscipy/_version.py
│ set build/lib.linux-x86_64-3.6/matscipy/_version.py to '0.3.0'
│ running build_ext
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ customize UnixCCompiler
│ customize UnixCCompiler using build_ext_subclass
│ building '_matscipy' extension
│ compiling C sources with arguments []
│ C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
│
│ creating build/temp.linux-x86_64-3.6
│ creating build/temp.linux-x86_64-3.6/c
│ compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
│ x86_64-linux-gnu-gcc: c/tools.c
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ c/tools.c:24:10: fatal error: Python.h: No such file or directory
│ #include <Python.h>
│ ^~~~~~~~~~
│ compilation terminated.
│ error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c c/tools.c -o build/temp.linux-x86_64-3.6/c/tools.o -MMD -MF build/temp.linux-x86_64-3.6/c/tools.o.d" failed with exit status 1
│ ----------------------------------------
│ ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2za64ax3/matscipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2za64ax3/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-wjnbnlbz/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/pkgeval/.local/include/python3.6m/matscipy Check the logs for full command output.
│ ERROR: LoadError: failed process: Process(`python3 -m pip install --upgrade --user matscipy`, ProcessExited(1)) [1]
│
│ Stacktrace:
│ [1] pipeline_error at ./process.jl:525 [inlined]
│ [2] run(::Cmd; wait::Bool) at ./process.jl:440
│ [3] run at ./process.jl:438 [inlined]
│ [4] pip(::String) at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:22
│ [5] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:44
│ [6] include(::String) at ./client.jl:441
│ [7] top-level scope at none:5
│ in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:28
│ caused by [exception 1]
│ PyError (PyImport_ImportModule
│
│ The Python package matscipy could not be found by pyimport. Usually this means
│ that you did not install matscipy in the Python version being used by PyCall.
│
│ PyCall is currently configured to use the Python version at:
│
│ /usr/bin/python3
│
│ and you should use whatever mechanism you usually use (apt-get, pip, conda,
│ etcetera) to install the Python package containing the matscipy module.
│
│ One alternative is to re-configure PyCall to use a different Python
│ version on your system: set ENV["PYTHON"] to the path/name of the python
│ executable you want to use, run Pkg.build("PyCall"), and re-launch Julia.
│
│ Another alternative is to configure PyCall to use a Julia-specific Python
│ distribution via the Conda.jl package (which installs a private Anaconda
│ Python distribution), which has the advantage that packages can be installed
│ and kept up-to-date via Julia. As explained in the PyCall documentation,
│ set ENV["PYTHON"]="", run Pkg.build("PyCall"), and re-launch Julia. Then,
│ To install the matscipy module, you can use `pyimport_conda("matscipy", PKG)`,
│ where PKG is the Anaconda package the contains the module matscipy,
│ or alternatively you can use the Conda package directly (via
│ `using Conda` followed by `Conda.add` etcetera).
│
│ ) <class 'ModuleNotFoundError'>
│ ModuleNotFoundError("No module named 'matscipy'",)
│
│ Stacktrace:
│ [1] pyimport(::String) at /home/pkgeval/.julia/packages/PyCall/zqDXB/src/PyCall.jl:536
│ [2] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/deps/build.jl:39
│ [3] include(::String) at ./client.jl:441
│ [4] top-level scope at none:5
│ Installing Dependencies of `ASE.jl`: `ase` and `matscipy`
│ `ase` was not found, trying to install via pip. If this fails,
│ please file an issue and try to install it manually, following
│ the instructions at `https://wiki.fysik.dtu.dk/ase/install.html`
│ I couldn't find `pip`. I will try to download and install it
│ automatically, but if this fails, please install
│ manually, then try to build `ASE` again.
│ `matscipy` was not found, trying to install it. If this fails,
│ please file an issue and try to install it manually, following
│ the instructions at `https://github.com/libAtoms/matscipy`
└ @ Pkg.Operations /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:912
Testing ASE
Status `/tmp/jl_Qx7nIm/Project.toml`
51974c44 ASE v0.5.1
945c410c JuLIP v0.8.2
2fcf5ba9 NeighbourLists v0.5.0
d96e819e Parameters v0.12.0
438e738f PyCall v1.91.4
189a3867 Reexport v0.2.0
37e2e46d LinearAlgebra
8dfed614 Test
Status `/tmp/jl_Qx7nIm/Manifest.toml`
51974c44 ASE v0.5.1
2169fc97 AlgebraicMultigrid v0.2.2
4fba245c ArrayInterface v2.5.1
b99e7846 BinaryProvider v0.5.8
49dc2e85 Calculus v0.5.1
bbf7d656 CommonSubexpressions v0.2.0
34da2185 Compat v2.2.0
e66e0078 CompilerSupportLibraries_jll v0.3.0+0
8f4d0f93 Conda v1.4.1
9a962f9c DataAPI v1.1.0
864edb3b DataStructures v0.17.10
39dd38d3 Dierckx v0.4.1
163ba53b DiffResults v1.0.2
b552c78f DiffRules v1.0.1
1a297f60 FillArrays v0.8.5
6a86dc24 FiniteDiff v2.2.1
f6369f11 ForwardDiff v0.10.9
069b7b12 FunctionWrappers v1.1.1
42fd0dbc IterativeSolvers v0.8.1
682c06a0 JSON v0.21.0
945c410c JuLIP v0.8.2
d3d80556 LineSearches v7.0.1
1914dd2f MacroTools v0.5.4
e1d29d7a Missings v0.4.3
d41bc354 NLSolversBase v7.6.1
77ba4419 NaNMath v0.3.3
2fcf5ba9 NeighbourLists v0.5.0
efe28fd5 OpenSpecFun_jll v0.5.3+3
429524aa Optim v0.20.1
bac558e1 OrderedCollections v1.1.0
d96e819e Parameters v0.12.0
69de0a69 Parsers v0.3.12
85a6dd25 PositiveFactorizations v0.2.3
438e738f PyCall v1.91.4
3cdcf5f2 RecipesBase v0.8.0
189a3867 Reexport v0.2.0
ae029012 Requires v1.0.1
a2af1166 SortingAlgorithms v0.3.1
276daf66 SpecialFunctions v0.10.0
90137ffa StaticArrays v0.12.1
2913bbd2 StatsBase v0.32.2
81def892 VersionParsing v1.2.0
2a0f44e3 Base64
ade2ca70 Dates
8bb1440f DelimitedFiles
8ba89e20 Distributed
b77e0a4c InteractiveUtils
76f85450 LibGit2
8f399da3 Libdl
37e2e46d LinearAlgebra
56ddb016 Logging
d6f4376e Markdown
a63ad114 Mmap
44cfe95a Pkg
de0858da Printf
3fa0cd96 REPL
9a3f8284 Random
ea8e919c SHA
9e88b42a Serialization
1a1011a3 SharedArrays
6462fe0b Sockets
2f01184e SparseArrays
10745b16 Statistics
4607b0f0 SuiteSparse
8dfed614 Test
cf7118a7 UUIDs
4ec0a83e Unicode
ERROR: LoadError: LoadError: LoadError: LoadError: PyError (PyImport_ImportModule
The Python package matscipy.neighbours could not be found by pyimport. Usually this means
that you did not install matscipy.neighbours in the Python version being used by PyCall.
PyCall is currently configured to use the Python version at:
/usr/bin/python3
and you should use whatever mechanism you usually use (apt-get, pip, conda,
etcetera) to install the Python package containing the matscipy.neighbours module.
One alternative is to re-configure PyCall to use a different Python
version on your system: set ENV["PYTHON"] to the path/name of the python
executable you want to use, run Pkg.build("PyCall"), and re-launch Julia.
Another alternative is to configure PyCall to use a Julia-specific Python
distribution via the Conda.jl package (which installs a private Anaconda
Python distribution), which has the advantage that packages can be installed
and kept up-to-date via Julia. As explained in the PyCall documentation,
set ENV["PYTHON"]="", run Pkg.build("PyCall"), and re-launch Julia. Then,
To install the matscipy.neighbours module, you can use `pyimport_conda("matscipy.neighbours", PKG)`,
where PKG is the Anaconda package the contains the module matscipy.neighbours,
or alternatively you can use the Conda package directly (via
`using Conda` followed by `Conda.add` etcetera).
) <class 'ModuleNotFoundError'>
ModuleNotFoundError("No module named 'matscipy'",)
Stacktrace:
[1] pyimport(::String) at /home/pkgeval/.julia/packages/PyCall/zqDXB/src/PyCall.jl:536
[2] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
[3] include(::Function, ::Module, ::String) at ./Base.jl:380
[4] include at ./Base.jl:368 [inlined]
[5] include(::String) at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[6] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/src/nlist.jl:7
[7] include(::Function, ::Module, ::String) at ./Base.jl:380
[8] include at ./Base.jl:368 [inlined]
[9] include(::String) at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:4
[10] top-level scope at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:355
[11] include(::Function, ::Module, ::String) at ./Base.jl:380
[12] include at ./Base.jl:368 [inlined]
[13] _require(::Base.PkgId) at ./loading.jl:1058
[14] require(::Base.PkgId) at ./loading.jl:927
[15] require(::Module, ::Symbol) at ./loading.jl:922
[16] include(::String) at ./client.jl:441
[17] top-level scope at none:6
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/src/MatSciPy.jl:23
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/src/nlist.jl:7
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/src/ASE.jl:355
in expression starting at /home/pkgeval/.julia/packages/ASE/GfCjR/test/runtests.jl:2
ERROR: Package ASE errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:53
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1523
[3] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:316
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:303
[5] #test#68 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[6] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[7] #test#67 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[8] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[10] test(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[11] top-level scope at none:13