unable to install biocode jinja2

[mchovat]

I am using MacOS. I have tried installing biocode but I keep running into an error. I have tried reinstalling igraph as well tried upgrading pip and changing permissions on the pip directory but I am still getting this error:

mchovat:dbs mrchovatia$ brew install igraph Warning: igraph 0.7.1_6 is already installed and up-to-date To reinstall 0.7.1_6, run brew reinstall igraph mchovat:dbs mrchovatia$ brew reinstall igraph ==> Reinstalling igraph ==> Downloading https://homebrew.bintray.com/bottles/igraph-0.7.1_6.mojave.bottle Already downloaded: /Users/mrchovatia/Library/Caches/Homebrew/downloads/e3aec1eec2b22327a31b3962a83834156f140ee5c0a592845483304cd085c05f--igraph-0.7.1_6.mojave.bottle.tar.gz ==> Pouring igraph-0.7.1_6.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/igraph/0.7.1_6: 85 files, 6MB mchovat:dbs mrchovatia$ sudo pip3 install biocode jinja2 The directory '/Users/mrchovatia/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. The directory '/Users/mrchovatia/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. Collecting biocode Downloading https://files.pythonhosted.org/packages/ac/58/b16f07e13b99403a0069b7782dc963882f634b6863d6e4bba85d327bd634/biocode-0.9.0.tar.gz (9.4MB) 100% |████████████████████████████████| 9.4MB 839kB/s Requirement already satisfied: jinja2 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (2.10.1) Collecting python-igraph (from biocode) Downloading https://files.pythonhosted.org/packages/0f/a0/4e7134f803737aa6eebb4e5250565ace0e2599659e22be7f7eba520ff017/python-igraph-0.7.1.post6.tar.gz (377kB) 100% |████████████████████████████████| 378kB 754kB/s Collecting matplotlib (from biocode) Downloading https://files.pythonhosted.org/packages/2e/81/bb51214944e79f9c9261badd7ef99b573fb0bc9110c0075c6a9e76224d0d/matplotlib-3.0.3-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (14.3MB) 100% |████████████████████████████████| 14.3MB 560kB/s Collecting taxadb (from biocode) Downloading https://files.pythonhosted.org/packages/f8/be/19e605b91abc7c6e3c6a183d89f1f6dca2c2851ba588f9673e77302934bc/taxadb-0.9.0-py3-none-any.whl Requirement already satisfied: MarkupSafe>=0.23 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from jinja2) (1.1.1) Requirement already satisfied: python-dateutil>=2.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from matplotlib->biocode) (2.8.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from matplotlib->biocode) (2.4.0) Collecting cycler>=0.10 (from matplotlib->biocode) Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl Collecting kiwisolver>=1.0.1 (from matplotlib->biocode) Downloading https://files.pythonhosted.org/packages/68/f2/21ec13269a420c063a3d7d8c87dac030da7b00fc6b27fa88cfb1c72a645b/kiwisolver-1.0.1-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (107kB) 100% |████████████████████████████████| 112kB 568kB/s Collecting numpy>=1.10.0 (from matplotlib->biocode) Downloading https://files.pythonhosted.org/packages/43/6e/71a3af8680a159a141fab5b4d19988111a09c02ffbfdeb42175cca0fa341/numpy-1.16.3-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.9MB) 100% |████████████████████████████████| 13.9MB 808kB/s Requirement already satisfied: requests in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from taxadb->biocode) (2.21.0) Collecting peewee==2.8.1 (from taxadb->biocode) Downloading https://files.pythonhosted.org/packages/59/4a/a1b78b0e47e880c07da21d633ff2ac8d5edbf969049a414edfbdadaed869/peewee-2.8.1.tar.gz (474kB) 100% |████████████████████████████████| 481kB 904kB/s Collecting tqdm (from taxadb->biocode) Downloading https://files.pythonhosted.org/packages/6c/4b/c38b5144cf167c4f52288517436ccafefe9dc01b8d1c190e18a6b154cd4a/tqdm-4.31.1-py2.py3-none-any.whl (48kB) 100% |████████████████████████████████| 51kB 778kB/s Requirement already satisfied: six>=1.5 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from python-dateutil>=2.1->matplotlib->biocode) (1.12.0) Requirement already satisfied: setuptools in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->biocode) (40.6.2) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from requests->taxadb->biocode) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from requests->taxadb->biocode) (2019.3.9) Requirement already satisfied: idna<2.9,>=2.5 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from requests->taxadb->biocode) (2.8) Requirement already satisfied: urllib3<1.25,>=1.21.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from requests->taxadb->biocode) (1.24.2) Installing collected packages: python-igraph, cycler, kiwisolver, numpy, matplotlib, peewee, tqdm, taxadb, biocode Running setup.py install for python-igraph ... error Complete output from command /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7 -u -c "import setuptools, tokenize;file='/private/tmp/pip-install-gcamzet7/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 /private/tmp/pip-record-up1h0e_a/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.macosx-10.9-x86_64-3.7 creating build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/configuration.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/clustering.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/compat.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/formula.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/layout.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/cut.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/init.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/matching.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/summary.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/datatypes.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/utils.py -> build/lib.macosx-10.9-x86_64-3.7/igraph copying igraph/statistics.py -> build/lib.macosx-10.9-x86_64-3.7/igraph creating build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/structural.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/colortests.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/attributes.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/rng.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/conversion.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/vertexseq.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/init.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/flow.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/games.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/matching.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/generators.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/isomorphism.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/basic.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/utils.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/edgeseq.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/decomposition.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/iterators.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/spectral.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/separators.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/homepage.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/atlas.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/indexing.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/operators.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/layouts.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/cliques.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/foreign.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test copying igraph/test/bipartite.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/test creating build/lib.macosx-10.9-x86_64-3.7/igraph/app copying igraph/app/shell.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/app copying igraph/app/init.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/app creating build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/shapes.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/edge.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/baseclasses.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/graph.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/coord.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/init.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/vertex.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/utils.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/text.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/metamagic.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing copying igraph/drawing/colors.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/drawing creating build/lib.macosx-10.9-x86_64-3.7/igraph/remote copying igraph/remote/init.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/remote copying igraph/remote/nexus.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/remote copying igraph/remote/gephi.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/remote creating build/lib.macosx-10.9-x86_64-3.7/igraph/vendor copying igraph/vendor/texttable.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/vendor copying igraph/vendor/init.py -> build/lib.macosx-10.9-x86_64-3.7/igraph/vendor Fixing build/lib.macosx-10.9-x86_64-3.7/igraph/configuration.py build/lib.macosx-10.9-x86_64-3.7/igraph/clustering.py build/lib.macosx-10.9-x86_64-3.7/igraph/compat.py build/lib.macosx-10.9-x86_64-3.7/igraph/formula.py build/lib.macosx-10.9-x86_64-3.7/igraph/layout.py build/lib.macosx-10.9-x86_64-3.7/igraph/cut.py build/lib.macosx-10.9-x86_64-3.7/igraph/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/matching.py build/lib.macosx-10.9-x86_64-3.7/igraph/summary.py build/lib.macosx-10.9-x86_64-3.7/igraph/datatypes.py build/lib.macosx-10.9-x86_64-3.7/igraph/utils.py build/lib.macosx-10.9-x86_64-3.7/igraph/statistics.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/structural.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/colortests.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/attributes.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/rng.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/conversion.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/vertexseq.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/flow.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/games.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/matching.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/generators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/isomorphism.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/basic.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/utils.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/edgeseq.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/decomposition.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/iterators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/spectral.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/separators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/homepage.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/atlas.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/indexing.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/operators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/layouts.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/cliques.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/foreign.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/bipartite.py build/lib.macosx-10.9-x86_64-3.7/igraph/app/shell.py build/lib.macosx-10.9-x86_64-3.7/igraph/app/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/shapes.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/edge.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/baseclasses.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/graph.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/coord.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/vertex.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/utils.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/text.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/metamagic.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/colors.py build/lib.macosx-10.9-x86_64-3.7/igraph/remote/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/remote/nexus.py build/lib.macosx-10.9-x86_64-3.7/igraph/remote/gephi.py build/lib.macosx-10.9-x86_64-3.7/igraph/vendor/texttable.py build/lib.macosx-10.9-x86_64-3.7/igraph/vendor/init.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing build/lib.macosx-10.9-x86_64-3.7/igraph/configuration.py build/lib.macosx-10.9-x86_64-3.7/igraph/clustering.py build/lib.macosx-10.9-x86_64-3.7/igraph/compat.py build/lib.macosx-10.9-x86_64-3.7/igraph/formula.py build/lib.macosx-10.9-x86_64-3.7/igraph/layout.py build/lib.macosx-10.9-x86_64-3.7/igraph/cut.py build/lib.macosx-10.9-x86_64-3.7/igraph/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/matching.py build/lib.macosx-10.9-x86_64-3.7/igraph/summary.py build/lib.macosx-10.9-x86_64-3.7/igraph/datatypes.py build/lib.macosx-10.9-x86_64-3.7/igraph/utils.py build/lib.macosx-10.9-x86_64-3.7/igraph/statistics.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/structural.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/colortests.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/attributes.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/rng.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/conversion.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/vertexseq.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/flow.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/games.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/matching.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/generators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/isomorphism.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/basic.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/utils.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/edgeseq.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/decomposition.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/iterators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/spectral.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/separators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/homepage.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/atlas.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/indexing.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/operators.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/layouts.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/cliques.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/foreign.py build/lib.macosx-10.9-x86_64-3.7/igraph/test/bipartite.py build/lib.macosx-10.9-x86_64-3.7/igraph/app/shell.py build/lib.macosx-10.9-x86_64-3.7/igraph/app/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/shapes.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/edge.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/baseclasses.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/graph.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/coord.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/vertex.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/utils.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/text.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/metamagic.py build/lib.macosx-10.9-x86_64-3.7/igraph/drawing/colors.py build/lib.macosx-10.9-x86_64-3.7/igraph/remote/init.py build/lib.macosx-10.9-x86_64-3.7/igraph/remote/nexus.py build/lib.macosx-10.9-x86_64-3.7/igraph/remote/gephi.py build/lib.macosx-10.9-x86_64-3.7/igraph/vendor/texttable.py build/lib.macosx-10.9-x86_64-3.7/igraph/vendor/init.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: 0.7.1.post6 We will also try: 0.7.1

Version 0.7.1.post6 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.

----------------------------------------

Command "/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7 -u -c "import setuptools, tokenize;file='/private/tmp/pip-install-gcamzet7/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 /private/tmp/pip-record-up1h0e_a/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-install-gcamzet7/python-igraph/ You are using pip version 18.1, however version 19.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

[jorvis]

This appears to be relevant. Could you try their suggestions?

https://github.com/igraph/python-igraph/issues/159

[mchovat]

I tried these commands: brew install igraph pip -v install python-igraph==0.7.1.post6

and got this error: InstallationError: Command "/usr/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/9d/63m3z36x70x86vrgpgpb_tnc0000gr/T/pip-install-8sFM5i/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 /private/var/folders/9d/63m3z36x70x86vrgpgpb_tnc0000gr/T/pip-record-N6cfEl/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/9d/63m3z36x70x86vrgpgpb_tnc0000gr/T/pip-install-8sFM5i/python-igraph/

Then I tried this command: sudo apt install build-essential python-dev libxml2 libxml2-dev zlib1g-dev

But then I got this: No Java runtime present, requesting install. I clicked OK and nothing happened.

[jorvis]

I'm afraid I don't have an OS X machine to test here. You'll need to search a bit about installing python-igraph on OS X. I found this from the source:

https://igraph.org/python/#pyinstallosx

[mchovat]

Ok thank you! I will try to look into this a bit more. Will post if something does end up working.

[jianlanren]

I have the same problem on my MacOS X. Please let me know if you get any solutions.

[jianlanren]

I tried uninstall jinja2 first and then re-install. $ pip uninstall jinja2 $ sudo pip install jinja2 It works for me and lets me go to the running step.

[mchovat]

Thank you. I did try that but it still doesn't work for me. I can't install Biocode.

[jorvis]

In case anyone reads this later, this came up again on a new laptop and doing this command first fixed it:

$ sudo apt install bison flex