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January 23, 2020 14:26
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Build log from mybinder.org for datacite/notebooks
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| Waiting for build to start... | |
| ---> Using cache | |
| ---> 46c9e2f973ca | |
| Step 45/71 : USER root | |
| ---> Using cache | |
| ---> 3e38e5418bfb | |
| Step 46/71 : RUN echo "options(repos = c(CRAN='https://mran.microsoft.com/snapshot/2019-04-12'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site | |
| ---> Using cache | |
| ---> b3773fa0d2e3 | |
| Step 47/71 : RUN install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid | |
| ---> Using cache | |
| ---> 5a970295b36a | |
| Step 48/71 : ARG REPO_DIR=${HOME} | |
| ---> Using cache | |
| ---> 2315ae318dbf | |
| Step 49/71 : ENV REPO_DIR ${REPO_DIR} | |
| ---> Using cache | |
| ---> 1aa1478a89ad | |
| Step 50/71 : WORKDIR ${REPO_DIR} | |
| ---> Using cache | |
| ---> 6235efcd3dd1 | |
| Step 51/71 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH} | |
| ---> Using cache | |
| ---> 7c2ceba32630 | |
| Step 52/71 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX} | |
| ---> Using cache | |
| ---> 0e6896405cce | |
| Step 53/71 : COPY src/install.R ${REPO_DIR}/install.R | |
| ---> Using cache | |
| ---> 43799d1eb449 | |
| Step 54/71 : COPY src/requirements.txt ${REPO_DIR}/requirements.txt | |
| ---> Using cache | |
| ---> 3605485b4317 | |
| Step 55/71 : USER root | |
| ---> Using cache | |
| ---> 452df57eb564 | |
| Step 56/71 : RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} | |
| ---> Using cache | |
| ---> 8481c06f6457 | |
| Step 57/71 : USER ${NB_USER} | |
| ---> Using cache | |
| ---> 9ac6859a3c68 | |
| Step 58/71 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt" | |
| ---> Running in 6efb65608470 | |
| Collecting certifi==2019.11.28 (from -r requirements.txt (line 1)) | |
| Downloading https://files.pythonhosted.org/packages/b9/63/df50cac98ea0d5b006c55a399c3bf1db9da7b5a24de7890bc9cfd5dd9e99/certifi-2019.11.28-py2.py3-none-any.whl (156kB) | |
| Requirement already satisfied: chardet==3.0.4 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (3.0.4) | |
| Collecting gql==0.1.0 (from -r requirements.txt (line 3)) | |
| Downloading https://files.pythonhosted.org/packages/aa/9c/2933b7791210e00f5c26a6243198cc03af9132c29cf85e4c22cb007f171e/gql-0.1.0.tar.gz | |
| Collecting graphql-core<3.0.0 (from -r requirements.txt (line 4)) | |
| Downloading https://files.pythonhosted.org/packages/6a/11/bc4a7eb440124271289d93e4d208bd07d94196038fabbe2a52435a07d3d3/graphql_core-2.2.1-py2.py3-none-any.whl (250kB) | |
| Requirement already satisfied: idna==2.8 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 5)) (2.8) | |
| Collecting promise==2.2.1 (from -r requirements.txt (line 6)) | |
| Downloading https://files.pythonhosted.org/packages/5a/81/221d09d90176fd90aed4b530e31b8fedf207385767c06d1d46c550c5e418/promise-2.2.1.tar.gz | |
| Collecting python-igraph==0.7 (from -r requirements.txt (line 7)) | |
| Downloading https://files.pythonhosted.org/packages/c4/c7/1f201917183d9292d40c34709393dcbea8a6510b0521ca6120605ecdbb1b/python-igraph-0.7.tar.gz (371kB) | |
| Requirement already satisfied: requests==2.22.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 8)) (2.22.0) | |
| Collecting six==1.13.0 (from -r requirements.txt (line 9)) | |
| Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl | |
| Collecting urllib3==1.25.7 (from -r requirements.txt (line 10)) | |
| Downloading https://files.pythonhosted.org/packages/b4/40/a9837291310ee1ccc242ceb6ebfd9eb21539649f193a7c8c86ba15b98539/urllib3-1.25.7-py2.py3-none-any.whl (125kB) | |
| Collecting rx<3,>=1.6 (from graphql-core<3.0.0->-r requirements.txt (line 4)) | |
| Downloading https://files.pythonhosted.org/packages/33/0f/5ef4ac78e2a538cc1b054eb86285fe0bf7a5dbaeaac2c584757c300515e2/Rx-1.6.1-py2.py3-none-any.whl (179kB) | |
| Building wheels for collected packages: gql, promise, python-igraph | |
| Building wheel for gql (setup.py): started | |
| Building wheel for gql (setup.py): finished with status 'done' | |
| Created wheel for gql: filename=gql-0.1.0-cp37-none-any.whl size=5541 sha256=15260fc64a00c0890fb13e43db22e8aa0ab77608bd55c0007ffe3405a3a5ec9e | |
| Stored in directory: /tmp/pip-ephem-wheel-cache-mcca9fzh/wheels/a7/8d/65/a3247f500d675d80a01e4d2f0ee44fe99f1faef575bc2a1664 | |
| Building wheel for promise (setup.py): started | |
| Building wheel for promise (setup.py): finished with status 'done' | |
| Created wheel for promise: filename=promise-2.2.1-cp37-none-any.whl size=21291 sha256=c46e40a583a8191811e2c3618a2f2a8821ab3e47acf069c41ddd3ac48af5b488 | |
| Stored in directory: /tmp/pip-ephem-wheel-cache-mcca9fzh/wheels/92/84/9f/75e2235effae0e1c5a5c0626a503e532bbffcb7e79e672b606 | |
| Building wheel for python-igraph (setup.py): started | |
| Building wheel for python-igraph (setup.py): finished with status 'error' | |
| ERROR: Command errored out with exit status 1: | |
| command: /srv/conda/envs/notebook/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1ugp56m2/python-igraph/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1ugp56m2/python-igraph/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-6x0f1dla --python-tag cp37 | |
| cwd: /tmp/pip-install-1ugp56m2/python-igraph/ | |
| Complete output (118 lines): | |
| running bdist_wheel | |
| running build | |
| running build_py | |
| creating build | |
| creating build/lib.linux-x86_64-3.7 | |
| creating build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/statistics.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/__init__.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/layout.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/configuration.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/compat.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/cut.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/utils.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/matching.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/summary.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/datatypes.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/clustering.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/formula.py -> build/lib.linux-x86_64-3.7/igraph | |
| creating build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/isomorphism.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/__init__.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/homepage.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/foreign.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/iterators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/edgeseq.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/games.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/generators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/flow.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/vertexseq.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/separators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/layouts.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/utils.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/structural.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/operators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/bipartite.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/rng.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/matching.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/cliques.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/indexing.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/conversion.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/atlas.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/decomposition.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/colortests.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/spectral.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/basic.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/attributes.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| creating build/lib.linux-x86_64-3.7/igraph/app | |
| copying igraph/app/__init__.py -> build/lib.linux-x86_64-3.7/igraph/app | |
| copying igraph/app/shell.py -> build/lib.linux-x86_64-3.7/igraph/app | |
| creating build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/edge.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/__init__.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/text.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/utils.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/vertex.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/shapes.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/coord.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/graph.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/colors.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/baseclasses.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/metamagic.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| creating build/lib.linux-x86_64-3.7/igraph/remote | |
| copying igraph/remote/__init__.py -> build/lib.linux-x86_64-3.7/igraph/remote | |
| copying igraph/remote/gephi.py -> build/lib.linux-x86_64-3.7/igraph/remote | |
| copying igraph/remote/nexus.py -> build/lib.linux-x86_64-3.7/igraph/remote | |
| creating build/lib.linux-x86_64-3.7/igraph/vendor | |
| copying igraph/vendor/__init__.py -> build/lib.linux-x86_64-3.7/igraph/vendor | |
| copying igraph/vendor/texttable.py -> build/lib.linux-x86_64-3.7/igraph/vendor | |
| Fixing build/lib.linux-x86_64-3.7/igraph/statistics.py build/lib.linux-x86_64-3.7/igraph/__init__.py build/lib.linux-x86_64-3.7/igraph/layout.py build/lib.linux-x86_64-3.7/igraph/configuration.py build/lib.linux-x86_64-3.7/igraph/compat.py build/lib.linux-x86_64-3.7/igraph/cut.py build/lib.linux-x86_64-3.7/igraph/utils.py build/lib.linux-x86_64-3.7/igraph/matching.py build/lib.linux-x86_64-3.7/igraph/summary.py build/lib.linux-x86_64-3.7/igraph/datatypes.py build/lib.linux-x86_64-3.7/igraph/clustering.py build/lib.linux-x86_64-3.7/igraph/formula.py build/lib.linux-x86_64-3.7/igraph/test/isomorphism.py build/lib.linux-x86_64-3.7/igraph/test/__init__.py build/lib.linux-x86_64-3.7/igraph/test/homepage.py build/lib.linux-x86_64-3.7/igraph/test/foreign.py build/lib.linux-x86_64-3.7/igraph/test/iterators.py build/lib.linux-x86_64-3.7/igraph/test/edgeseq.py build/lib.linux-x86_64-3.7/igraph/test/games.py build/lib.linux-x86_64-3.7/igraph/test/generators.py build/lib.linux-x86_64-3.7/igraph/test/flow.py build/lib.linux-x86_64-3.7/igraph/test/vertexseq.py build/lib.linux-x86_64-3.7/igraph/test/separators.py build/lib.linux-x86_64-3.7/igraph/test/layouts.py build/lib.linux-x86_64-3.7/igraph/test/utils.py build/lib.linux-x86_64-3.7/igraph/test/structural.py build/lib.linux-x86_64-3.7/igraph/test/operators.py build/lib.linux-x86_64-3.7/igraph/test/bipartite.py build/lib.linux-x86_64-3.7/igraph/test/rng.py build/lib.linux-x86_64-3.7/igraph/test/matching.py build/lib.linux-x86_64-3.7/igraph/test/cliques.py build/lib.linux-x86_64-3.7/igraph/test/indexing.py build/lib.linux-x86_64-3.7/igraph/test/conversion.py build/lib.linux-x86_64-3.7/igraph/test/atlas.py build/lib.linux-x86_64-3.7/igraph/test/decomposition.py build/lib.linux-x86_64-3.7/igraph/test/colortests.py build/lib.linux-x86_64-3.7/igraph/test/spectral.py build/lib.linux-x86_64-3.7/igraph/test/basic.py build/lib.linux-x86_64-3.7/igraph/test/attributes.py build/lib.linux-x86_64-3.7/igraph/app/__init__.py build/lib.linux-x86_64-3.7/igraph/app/shell.py build/lib.linux-x86_64-3.7/igraph/drawing/edge.py build/lib.linux-x86_64-3.7/igraph/drawing/__init__.py build/lib.linux-x86_64-3.7/igraph/drawing/text.py build/lib.linux-x86_64-3.7/igraph/drawing/utils.py build/lib.linux-x86_64-3.7/igraph/drawing/vertex.py build/lib.linux-x86_64-3.7/igraph/drawing/shapes.py build/lib.linux-x86_64-3.7/igraph/drawing/coord.py build/lib.linux-x86_64-3.7/igraph/drawing/graph.py build/lib.linux-x86_64-3.7/igraph/drawing/colors.py build/lib.linux-x86_64-3.7/igraph/drawing/baseclasses.py build/lib.linux-x86_64-3.7/igraph/drawing/metamagic.py build/lib.linux-x86_64-3.7/igraph/remote/__init__.py build/lib.linux-x86_64-3.7/igraph/remote/gephi.py build/lib.linux-x86_64-3.7/igraph/remote/nexus.py build/lib.linux-x86_64-3.7/igraph/vendor/__init__.py build/lib.linux-x86_64-3.7/igraph/vendor/texttable.py | |
| Skipping optional fixer: buffer | |
| Skipping optional fixer: idioms | |
| Skipping optional fixer: set_literal | |
| Skipping optional fixer: ws_comma | |
| Fixing build/lib.linux-x86_64-3.7/igraph/statistics.py build/lib.linux-x86_64-3.7/igraph/__init__.py build/lib.linux-x86_64-3.7/igraph/layout.py build/lib.linux-x86_64-3.7/igraph/configuration.py build/lib.linux-x86_64-3.7/igraph/compat.py build/lib.linux-x86_64-3.7/igraph/cut.py build/lib.linux-x86_64-3.7/igraph/utils.py build/lib.linux-x86_64-3.7/igraph/matching.py build/lib.linux-x86_64-3.7/igraph/summary.py build/lib.linux-x86_64-3.7/igraph/datatypes.py build/lib.linux-x86_64-3.7/igraph/clustering.py build/lib.linux-x86_64-3.7/igraph/formula.py build/lib.linux-x86_64-3.7/igraph/test/isomorphism.py build/lib.linux-x86_64-3.7/igraph/test/__init__.py build/lib.linux-x86_64-3.7/igraph/test/homepage.py build/lib.linux-x86_64-3.7/igraph/test/foreign.py build/lib.linux-x86_64-3.7/igraph/test/iterators.py build/lib.linux-x86_64-3.7/igraph/test/edgeseq.py build/lib.linux-x86_64-3.7/igraph/test/games.py build/lib.linux-x86_64-3.7/igraph/test/generators.py build/lib.linux-x86_64-3.7/igraph/test/flow.py build/lib.linux-x86_64-3.7/igraph/test/vertexseq.py build/lib.linux-x86_64-3.7/igraph/test/separators.py build/lib.linux-x86_64-3.7/igraph/test/layouts.py build/lib.linux-x86_64-3.7/igraph/test/utils.py build/lib.linux-x86_64-3.7/igraph/test/structural.py build/lib.linux-x86_64-3.7/igraph/test/operators.py build/lib.linux-x86_64-3.7/igraph/test/bipartite.py build/lib.linux-x86_64-3.7/igraph/test/rng.py build/lib.linux-x86_64-3.7/igraph/test/matching.py build/lib.linux-x86_64-3.7/igraph/test/cliques.py build/lib.linux-x86_64-3.7/igraph/test/indexing.py build/lib.linux-x86_64-3.7/igraph/test/conversion.py build/lib.linux-x86_64-3.7/igraph/test/atlas.py build/lib.linux-x86_64-3.7/igraph/test/decomposition.py build/lib.linux-x86_64-3.7/igraph/test/colortests.py build/lib.linux-x86_64-3.7/igraph/test/spectral.py build/lib.linux-x86_64-3.7/igraph/test/basic.py build/lib.linux-x86_64-3.7/igraph/test/attributes.py build/lib.linux-x86_64-3.7/igraph/app/__init__.py build/lib.linux-x86_64-3.7/igraph/app/shell.py build/lib.linux-x86_64-3.7/igraph/drawing/edge.py build/lib.linux-x86_64-3.7/igraph/drawing/__init__.py build/lib.linux-x86_64-3.7/igraph/drawing/text.py build/lib.linux-x86_64-3.7/igraph/drawing/utils.py build/lib.linux-x86_64-3.7/igraph/drawing/vertex.py build/lib.linux-x86_64-3.7/igraph/drawing/shapes.py build/lib.linux-x86_64-3.7/igraph/drawing/coord.py build/lib.linux-x86_64-3.7/igraph/drawing/graph.py build/lib.linux-x86_64-3.7/igraph/drawing/colors.py build/lib.linux-x86_64-3.7/igraph/drawing/baseclasses.py build/lib.linux-x86_64-3.7/igraph/drawing/metamagic.py build/lib.linux-x86_64-3.7/igraph/remote/__init__.py build/lib.linux-x86_64-3.7/igraph/remote/gephi.py build/lib.linux-x86_64-3.7/igraph/remote/nexus.py build/lib.linux-x86_64-3.7/igraph/vendor/__init__.py build/lib.linux-x86_64-3.7/igraph/vendor/texttable.py | |
| Skipping optional fixer: buffer | |
| Skipping optional fixer: idioms | |
| Skipping optional fixer: set_literal | |
| Skipping optional fixer: ws_comma | |
| running build_ext | |
| Cannot find the C core of igraph on this system using pkg-config. | |
| We will now try to download and compile the C core from scratch. | |
| Version number of the C core: 0.7 | |
| We will also try: 0.7.0 | |
| Version 0.7 of the C core of igraph is not found among the nightly builds. | |
| Use the --c-core-version switch to try a different version. | |
| Could not download and compile the C core of igraph. | |
| WARNING: we were not able to detect where igraph is installed on | |
| your machine (if it is installed at all). We will use the fallback | |
| library and include pathss hardcoded in setup.py and hope that the | |
| C core of igraph is installed there. | |
| If the compilation fails and you are sure that igraph is installed | |
| on your machine, adjust the following two variables in setup.py | |
| accordingly and try again: | |
| - LIBIGRAPH_FALLBACK_INCLUDE_DIRS | |
| - LIBIGRAPH_FALLBACK_LIBRARY_DIRS | |
| Build type: dynamic extension | |
| Include path: /usr/include/igraph /usr/local/include/igraph | |
| Library path: | |
| Linked dynamic libraries: igraph | |
| Linked static libraries: | |
| Extra compiler options: | |
| Extra linker options: | |
| building 'igraph._igraph' extension | |
| creating build/temp.linux-x86_64-3.7 | |
| creating build/temp.linux-x86_64-3.7/src | |
| gcc -pthread -B /srv/conda/envs/notebook/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/igraph -I/usr/local/include/igraph -I../../build/include -I../../include -I/usr/local/include/igraph -I/usr/include/igraph -I/srv/conda/envs/notebook/include/python3.7m -c src/edgeobject.c -o build/temp.linux-x86_64-3.7/src/edgeobject.o | |
| In file included from src/edgeobject.c:25:0: | |
| src/attributes.h:27:10: fatal error: igraph_attributes.h: No such file or directory | |
| #include <igraph_attributes.h> | |
| ^~~~~~~~~~~~~~~~~~~~~ | |
| compilation terminated. | |
| error: command 'gcc' failed with exit status 1 | |
| ---------------------------------------- | |
| ERROR: Failed building wheel for python-igraph | |
| Running setup.py clean for python-igraph | |
| Successfully built gql promise | |
| Failed to build python-igraph | |
| Installing collected packages: certifi, six, promise, rx, graphql-core, gql, python-igraph, urllib3 | |
| Found existing installation: certifi 2019.9.11 | |
| Uninstalling certifi-2019.9.11: | |
| Successfully uninstalled certifi-2019.9.11 | |
| Found existing installation: six 1.12.0 | |
| Uninstalling six-1.12.0: | |
| Successfully uninstalled six-1.12.0 | |
| Running setup.py install for python-igraph: started | |
| Running setup.py install for python-igraph: finished with status 'error' | |
| ERROR: Command errored out with exit status 1: | |
| command: /srv/conda/envs/notebook/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1ugp56m2/python-igraph/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1ugp56m2/python-igraph/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-u6w4nt00/install-record.txt --single-version-externally-managed --compile | |
| cwd: /tmp/pip-install-1ugp56m2/python-igraph/ | |
| Complete output (118 lines): | |
| running install | |
| running build | |
| running build_py | |
| creating build | |
| creating build/lib.linux-x86_64-3.7 | |
| creating build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/statistics.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/__init__.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/layout.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/configuration.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/compat.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/cut.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/utils.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/matching.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/summary.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/datatypes.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/clustering.py -> build/lib.linux-x86_64-3.7/igraph | |
| copying igraph/formula.py -> build/lib.linux-x86_64-3.7/igraph | |
| creating build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/isomorphism.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/__init__.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/homepage.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/foreign.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/iterators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/edgeseq.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/games.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/generators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/flow.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/vertexseq.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/separators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/layouts.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/utils.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/structural.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/operators.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/bipartite.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/rng.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/matching.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/cliques.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/indexing.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/conversion.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/atlas.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/decomposition.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/colortests.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/spectral.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/basic.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| copying igraph/test/attributes.py -> build/lib.linux-x86_64-3.7/igraph/test | |
| creating build/lib.linux-x86_64-3.7/igraph/app | |
| copying igraph/app/__init__.py -> build/lib.linux-x86_64-3.7/igraph/app | |
| copying igraph/app/shell.py -> build/lib.linux-x86_64-3.7/igraph/app | |
| creating build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/edge.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/__init__.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/text.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/utils.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/vertex.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/shapes.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/coord.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/graph.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/colors.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/baseclasses.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| copying igraph/drawing/metamagic.py -> build/lib.linux-x86_64-3.7/igraph/drawing | |
| creating build/lib.linux-x86_64-3.7/igraph/remote | |
| copying igraph/remote/__init__.py -> build/lib.linux-x86_64-3.7/igraph/remote | |
| copying igraph/remote/gephi.py -> build/lib.linux-x86_64-3.7/igraph/remote | |
| copying igraph/remote/nexus.py -> build/lib.linux-x86_64-3.7/igraph/remote | |
| creating build/lib.linux-x86_64-3.7/igraph/vendor | |
| copying igraph/vendor/__init__.py -> build/lib.linux-x86_64-3.7/igraph/vendor | |
| copying igraph/vendor/texttable.py -> build/lib.linux-x86_64-3.7/igraph/vendor | |
| Fixing build/lib.linux-x86_64-3.7/igraph/statistics.py build/lib.linux-x86_64-3.7/igraph/__init__.py build/lib.linux-x86_64-3.7/igraph/layout.py build/lib.linux-x86_64-3.7/igraph/configuration.py build/lib.linux-x86_64-3.7/igraph/compat.py build/lib.linux-x86_64-3.7/igraph/cut.py build/lib.linux-x86_64-3.7/igraph/utils.py build/lib.linux-x86_64-3.7/igraph/matching.py build/lib.linux-x86_64-3.7/igraph/summary.py build/lib.linux-x86_64-3.7/igraph/datatypes.py build/lib.linux-x86_64-3.7/igraph/clustering.py build/lib.linux-x86_64-3.7/igraph/formula.py build/lib.linux-x86_64-3.7/igraph/test/isomorphism.py build/lib.linux-x86_64-3.7/igraph/test/__init__.py build/lib.linux-x86_64-3.7/igraph/test/homepage.py build/lib.linux-x86_64-3.7/igraph/test/foreign.py build/lib.linux-x86_64-3.7/igraph/test/iterators.py build/lib.linux-x86_64-3.7/igraph/test/edgeseq.py build/lib.linux-x86_64-3.7/igraph/test/games.py build/lib.linux-x86_64-3.7/igraph/test/generators.py build/lib.linux-x86_64-3.7/igraph/test/flow.py build/lib.linux-x86_64-3.7/igraph/test/vertexseq.py build/lib.linux-x86_64-3.7/igraph/test/separators.py build/lib.linux-x86_64-3.7/igraph/test/layouts.py build/lib.linux-x86_64-3.7/igraph/test/utils.py build/lib.linux-x86_64-3.7/igraph/test/structural.py build/lib.linux-x86_64-3.7/igraph/test/operators.py build/lib.linux-x86_64-3.7/igraph/test/bipartite.py build/lib.linux-x86_64-3.7/igraph/test/rng.py build/lib.linux-x86_64-3.7/igraph/test/matching.py build/lib.linux-x86_64-3.7/igraph/test/cliques.py build/lib.linux-x86_64-3.7/igraph/test/indexing.py build/lib.linux-x86_64-3.7/igraph/test/conversion.py build/lib.linux-x86_64-3.7/igraph/test/atlas.py build/lib.linux-x86_64-3.7/igraph/test/decomposition.py build/lib.linux-x86_64-3.7/igraph/test/colortests.py build/lib.linux-x86_64-3.7/igraph/test/spectral.py build/lib.linux-x86_64-3.7/igraph/test/basic.py build/lib.linux-x86_64-3.7/igraph/test/attributes.py build/lib.linux-x86_64-3.7/igraph/app/__init__.py build/lib.linux-x86_64-3.7/igraph/app/shell.py build/lib.linux-x86_64-3.7/igraph/drawing/edge.py build/lib.linux-x86_64-3.7/igraph/drawing/__init__.py build/lib.linux-x86_64-3.7/igraph/drawing/text.py build/lib.linux-x86_64-3.7/igraph/drawing/utils.py build/lib.linux-x86_64-3.7/igraph/drawing/vertex.py build/lib.linux-x86_64-3.7/igraph/drawing/shapes.py build/lib.linux-x86_64-3.7/igraph/drawing/coord.py build/lib.linux-x86_64-3.7/igraph/drawing/graph.py build/lib.linux-x86_64-3.7/igraph/drawing/colors.py build/lib.linux-x86_64-3.7/igraph/drawing/baseclasses.py build/lib.linux-x86_64-3.7/igraph/drawing/metamagic.py build/lib.linux-x86_64-3.7/igraph/remote/__init__.py build/lib.linux-x86_64-3.7/igraph/remote/gephi.py build/lib.linux-x86_64-3.7/igraph/remote/nexus.pybuild/lib.linux-x86_64-3.7/igraph/vendor/__init__.py build/lib.linux-x86_64-3.7/igraph/vendor/texttable.py | |
| Skipping optional fixer: buffer | |
| Skipping optional fixer: idioms | |
| Skipping optional fixer: set_literal | |
| Skipping optional fixer: ws_comma | |
| Fixing build/lib.linux-x86_64-3.7/igraph/statistics.py build/lib.linux-x86_64-3.7/igraph/__init__.py build/lib.linux-x86_64-3.7/igraph/layout.py build/lib.linux-x86_64-3.7/igraph/configuration.py build/lib.linux-x86_64-3.7/igraph/compat.py build/lib.linux-x86_64-3.7/igraph/cut.py build/lib.linux-x86_64-3.7/igraph/utils.py build/lib.linux-x86_64-3.7/igraph/matching.py build/lib.linux-x86_64-3.7/igraph/summary.py build/lib.linux-x86_64-3.7/igraph/datatypes.py build/lib.linux-x86_64-3.7/igraph/clustering.py build/lib.linux-x86_64-3.7/igraph/formula.py build/lib.linux-x86_64-3.7/igraph/test/isomorphism.py build/lib.linux-x86_64-3.7/igraph/test/__init__.py build/lib.linux-x86_64-3.7/igraph/test/homepage.py build/lib.linux-x86_64-3.7/igraph/test/foreign.py build/lib.linux-x86_64-3.7/igraph/test/iterators.py build/lib.linux-x86_64-3.7/igraph/test/edgeseq.py build/lib.linux-x86_64-3.7/igraph/test/games.py build/lib.linux-x86_64-3.7/igraph/test/generators.py build/lib.linux-x86_64-3.7/igraph/test/flow.py build/lib.linux-x86_64-3.7/igraph/test/vertexseq.py build/lib.linux-x86_64-3.7/igraph/test/separators.py build/lib.linux-x86_64-3.7/igraph/test/layouts.py build/lib.linux-x86_64-3.7/igraph/test/utils.py build/lib.linux-x86_64-3.7/igraph/test/structural.py build/lib.linux-x86_64-3.7/igraph/test/operators.py build/lib.linux-x86_64-3.7/igraph/test/bipartite.py build/lib.linux-x86_64-3.7/igraph/test/rng.py build/lib.linux-x86_64-3.7/igraph/test/matching.py build/lib.linux-x86_64-3.7/igraph/test/cliques.py build/lib.linux-x86_64-3.7/igraph/test/indexing.py build/lib.linux-x86_64-3.7/igraph/test/conversion.py build/lib.linux-x86_64-3.7/igraph/test/atlas.py build/lib.linux-x86_64-3.7/igraph/test/decomposition.py build/lib.linux-x86_64-3.7/igraph/test/colortests.py build/lib.linux-x86_64-3.7/igraph/test/spectral.py build/lib.linux-x86_64-3.7/igraph/test/basic.py build/lib.linux-x86_64-3.7/igraph/test/attributes.py build/lib.linux-x86_64-3.7/igraph/app/__init__.py build/lib.linux-x86_64-3.7/igraph/app/shell.py build/lib.linux-x86_64-3.7/igraph/drawing/edge.py build/lib.linux-x86_64-3.7/igraph/drawing/__init__.py build/lib.linux-x86_64-3.7/igraph/drawing/text.py build/lib.linux-x86_64-3.7/igraph/drawing/utils.py build/lib.linux-x86_64-3.7/igraph/drawing/vertex.py build/lib.linux-x86_64-3.7/igraph/drawing/shapes.py build/lib.linux-x86_64-3.7/igraph/drawing/coord.py build/lib.linux-x86_64-3.7/igraph/drawing/graph.py build/lib.linux-x86_64-3.7/igraph/drawing/colors.py build/lib.linux-x86_64-3.7/igraph/drawing/baseclasses.py build/lib.linux-x86_64-3.7/igraph/drawing/metamagic.py build/lib.linux-x86_64-3.7/igraph/remote/__init__.py build/lib.linux-x86_64-3.7/igraph/remote/gephi.py build/lib.linux-x86_64-3.7/igraph/remote/nexus.pybuild/lib.linux-x86_64-3.7/igraph/vendor/__init__.py build/lib.linux-x86_64-3.7/igraph/vendor/texttable.py | |
| Skipping optional fixer: buffer | |
| Skipping optional fixer: idioms | |
| Skipping optional fixer: set_literal | |
| Skipping optional fixer: ws_comma | |
| running build_ext | |
| Cannot find the C core of igraph on this system using pkg-config. | |
| We will now try to download and compile the C core from scratch. | |
| Version number of the C core: 0.7 | |
| We will also try: 0.7.0 | |
| Version 0.7 of the C core of igraph is not found among the nightly builds. | |
| Use the --c-core-version switch to try a different version. | |
| Could not download and compile the C core of igraph. | |
| WARNING: we were not able to detect where igraph is installed on | |
| your machine (if it is installed at all). We will use the fallback | |
| library and include pathss hardcoded in setup.py and hope that the | |
| C core of igraph is installed there. | |
| If the compilation fails and you are sure that igraph is installed | |
| on your machine, adjust the following two variables in setup.py | |
| accordingly and try again: | |
| - LIBIGRAPH_FALLBACK_INCLUDE_DIRS | |
| - LIBIGRAPH_FALLBACK_LIBRARY_DIRS | |
| Build type: dynamic extension | |
| Include path: /usr/include/igraph /usr/local/include/igraph | |
| Library path: | |
| Linked dynamic libraries: igraph | |
| Linked static libraries: | |
| Extra compiler options: | |
| Extra linker options: | |
| building 'igraph._igraph' extension | |
| creating build/temp.linux-x86_64-3.7 | |
| creating build/temp.linux-x86_64-3.7/src | |
| gcc -pthread -B /srv/conda/envs/notebook/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/igraph -I/usr/local/include/igraph -I../../build/include -I../../include -I/usr/local/include/igraph -I/usr/include/igraph -I/srv/conda/envs/notebook/include/python3.7m -c src/edgeobject.c -o build/temp.linux-x86_64-3.7/src/edgeobject.o | |
| In file included from src/edgeobject.c:25:0: | |
| src/attributes.h:27:10: fatal error: igraph_attributes.h: No such file or directory | |
| #include <igraph_attributes.h> | |
| ^~~~~~~~~~~~~~~~~~~~~ | |
| compilation terminated. | |
| error: command 'gcc' failed with exit status 1 | |
| ---------------------------------------- | |
| ERROR: Command errored out with exit status 1: /srv/conda/envs/notebook/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1ugp56m2/python-igraph/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1ugp56m2/python-igraph/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-u6w4nt00/install-record.txt --single-version-externally-managed --compile Check the logs for full command output. | |
| Removing intermediate container 6efb65608470 | |
| The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"' returned a non-zero code: 1 |
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