search

galaxyproject / ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.
https://ephemeris.readthedocs.org/
Other
28 stars 38 forks source link

Failed to build future for https://training.galaxyproject.org/training-material/topics/admin/tutorials/tool-management/tutorial.html#hands-on-installing-ephemeris-in-a-python-virtual-environment #207

Closed j34ni closed 7 months ago

j34ni commented 7 months ago

On a VM with Ubuntu 20.04.6 LTS installing Ephemeris in a Python virtual environment failed with this error:

pip install ephemeris
Collecting ephemeris
  Downloading ephemeris-0.10.8-py2.py3-none-any.whl (44 kB)
     |████████████████████████████████| 44 kB 2.2 MB/s 
Collecting bioblend>=0.10.0
  Downloading bioblend-1.2.0-py2.py3-none-any.whl (156 kB)
     |████████████████████████████████| 156 kB 13.3 MB/s 
Collecting galaxy-tool-util>=20.9.1
  Downloading galaxy_tool_util-23.1.1-py3-none-any.whl (404 kB)
     |████████████████████████████████| 404 kB 120.2 MB/s 
Collecting galaxy-util>=20.9.0
  Downloading galaxy_util-23.1.1-py3-none-any.whl (122 kB)
     |████████████████████████████████| 122 kB 135.5 MB/s 
Collecting pysam
  Downloading pysam-0.22.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (21.8 MB)
     |████████████████████████████████| 21.8 MB 63.0 MB/s 
Collecting six>=1.9.0
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting Jinja2
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     |████████████████████████████████| 133 kB 128.0 MB/s 
Collecting PyYAML
  Downloading PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (736 kB)
     |████████████████████████████████| 736 kB 97.3 MB/s 
Collecting rich
  Downloading rich-13.7.0-py3-none-any.whl (240 kB)
     |████████████████████████████████| 240 kB 124.3 MB/s 
Collecting typing-extensions
  Downloading typing_extensions-4.8.0-py3-none-any.whl (31 kB)
Collecting tuspy
  Downloading tuspy-1.0.1-py3-none-any.whl (14 kB)
Collecting requests>=2.20.0
  Downloading requests-2.31.0-py3-none-any.whl (62 kB)
     |████████████████████████████████| 62 kB 1.6 MB/s 
Collecting requests-toolbelt!=0.9.0,>=0.5.1
  Downloading requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB)
     |████████████████████████████████| 54 kB 4.3 MB/s 
Collecting lxml
  Downloading lxml-4.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (7.1 MB)
     |████████████████████████████████| 7.1 MB 113.2 MB/s 
Collecting sortedcontainers
  Downloading sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting conda-package-streaming
  Downloading conda_package_streaming-0.9.0-py3-none-any.whl (15 kB)
Collecting pydantic<2
  Downloading pydantic-1.10.13-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
     |████████████████████████████████| 3.2 MB 111.9 MB/s 
Collecting packaging
  Downloading packaging-23.2-py3-none-any.whl (53 kB)
     |████████████████████████████████| 53 kB 907 kB/s 
Collecting MarkupSafe
  Downloading MarkupSafe-2.1.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting importlib-resources
  Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Collecting Routes
  Downloading Routes-2.5.1-py2.py3-none-any.whl (40 kB)
     |████████████████████████████████| 40 kB 5.8 MB/s 
Collecting pyparsing
  Downloading pyparsing-3.1.1-py3-none-any.whl (103 kB)
     |████████████████████████████████| 103 kB 124.6 MB/s 
Collecting docutils
  Downloading docutils-0.20.1-py3-none-any.whl (572 kB)
     |████████████████████████████████| 572 kB 122.4 MB/s 
Collecting bleach
  Downloading bleach-6.1.0-py3-none-any.whl (162 kB)
     |████████████████████████████████| 162 kB 127.5 MB/s 
Collecting zipstream-new
  Downloading zipstream_new-1.1.8-py3-none-any.whl (20 kB)
Collecting boltons
  Downloading boltons-23.1.1-py2.py3-none-any.whl (195 kB)
     |████████████████████████████████| 195 kB 119.4 MB/s 
Collecting markdown-it-py>=2.2.0
  Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
     |████████████████████████████████| 87 kB 6.0 MB/s 
Collecting pygments<3.0.0,>=2.13.0
  Downloading Pygments-2.16.1-py3-none-any.whl (1.2 MB)
     |████████████████████████████████| 1.2 MB 114.4 MB/s 
Collecting aiohttp>=3.6.2
  Downloading aiohttp-3.8.6-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     |████████████████████████████████| 1.1 MB 103.1 MB/s 
Collecting tinydb>=3.5.0
  Downloading tinydb-4.8.0-py3-none-any.whl (24 kB)
Collecting future>=0.16.0
  Downloading future-0.18.3.tar.gz (840 kB)
     |████████████████████████████████| 840 kB 120.7 MB/s 
Collecting certifi>=2017.4.17
  Downloading certifi-2023.7.22-py3-none-any.whl (158 kB)
     |████████████████████████████████| 158 kB 122.5 MB/s 
Collecting charset-normalizer<4,>=2
  Downloading charset_normalizer-3.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (141 kB)
     |████████████████████████████████| 141 kB 125.5 MB/s 
Collecting urllib3<3,>=1.21.1
  Downloading urllib3-2.1.0-py3-none-any.whl (104 kB)
     |████████████████████████████████| 104 kB 136.0 MB/s 
Collecting idna<4,>=2.5
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     |████████████████████████████████| 61 kB 71 kB/s 
Collecting zstandard>=0.15
  Downloading zstandard-0.22.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
     |████████████████████████████████| 5.4 MB 122.0 MB/s 
Collecting zipp>=3.1.0; python_version < "3.10"
  Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
Collecting repoze.lru>=0.3
  Downloading repoze.lru-0.7-py3-none-any.whl (10 kB)
Collecting webencodings
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting mdurl~=0.1
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Collecting aiosignal>=1.1.2
  Downloading aiosignal-1.3.1-py3-none-any.whl (7.6 kB)
Collecting async-timeout<5.0,>=4.0.0a3
  Downloading async_timeout-4.0.3-py3-none-any.whl (5.7 kB)
Collecting attrs>=17.3.0
  Downloading attrs-23.1.0-py3-none-any.whl (61 kB)
     |████████████████████████████████| 61 kB 10.4 MB/s 
Collecting yarl<2.0,>=1.0
  Downloading yarl-1.9.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (266 kB)
     |████████████████████████████████| 266 kB 116.1 MB/s 
Collecting frozenlist>=1.1.1
  Downloading frozenlist-1.4.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (220 kB)
     |████████████████████████████████| 220 kB 112.6 MB/s 
Collecting multidict<7.0,>=4.5
  Downloading multidict-6.0.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (121 kB)
     |████████████████████████████████| 121 kB 134.0 MB/s 
Building wheels for collected packages: future
  Building wheel for future (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/ubuntu/ephemeris_venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xi9n5iro/future/setup.py'"'"'; __file__='"'"'/tmp/pip-install-xi9n5iro/future/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-9hbbz_c1
       cwd: /tmp/pip-install-xi9n5iro/future/
  Complete output (6 lines):
  usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: setup.py --help [cmd1 cmd2 ...]
     or: setup.py --help-commands
     or: setup.py cmd --help

  error: invalid command 'bdist_wheel'
  ----------------------------------------
  ERROR: Failed building wheel for future
  Running setup.py clean for future
Failed to build future
Installing collected packages: typing-extensions, frozenlist, aiosignal, async-timeout, attrs, charset-normalizer, multidict, idna, yarl, aiohttp, tinydb, certifi, urllib3, requests, future, six, tuspy, requests-toolbelt, bioblend, lxml, sortedcontainers, zstandard, conda-package-streaming, pydantic, packaging, zipp, importlib-resources, repoze.lru, Routes, pyparsing, docutils, webencodings, bleach, zipstream-new, PyYAML, boltons, galaxy-util, MarkupSafe, galaxy-tool-util, pysam, Jinja2, mdurl, markdown-it-py, pygments, rich, ephemeris
    Running setup.py install for future ... done
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 PyYAML-6.0.1 Routes-2.5.1 aiohttp-3.8.6 aiosignal-1.3.1 async-timeout-4.0.3 attrs-23.1.0 bioblend-1.2.0 bleach-6.1.0 boltons-23.1.1 certifi-2023.7.22 charset-normalizer-3.3.2 conda-package-streaming-0.9.0 docutils-0.20.1 ephemeris-0.10.8 frozenlist-1.4.0 future-0.18.3 galaxy-tool-util-23.1.1 galaxy-util-23.1.1 idna-3.4 importlib-resources-6.1.1 lxml-4.9.3 markdown-it-py-3.0.0 mdurl-0.1.2 multidict-6.0.4 packaging-23.2 pydantic-1.10.13 pygments-2.16.1 pyparsing-3.1.1 pysam-0.22.0 repoze.lru-0.7 requests-2.31.0 requests-toolbelt-1.0.0 rich-13.7.0 six-1.16.0 sortedcontainers-2.4.0 tinydb-4.8.0 tuspy-1.0.1 typing-extensions-4.8.0 urllib3-2.1.0 webencodings-0.5.1 yarl-1.9.2 zipp-3.17.0 zipstream-new-1.1.8 zstandard-0.22.0
mvdbeek commented 7 months ago

We're not bringing in future, I don't think this is the right place to report this

j34ni commented 7 months ago

Perhaps, but is it likely to affect the remainder of the deployment or should I simply ignore it?

mvdbeek commented 7 months ago

I don't know, I think the fix for you is to install wheel maybe ? https://stackoverflow.com/a/44862371

j34ni commented 7 months ago

Thanks, I will try that if something else fails in the next steps