installation problems

[LidiaML]

Dear all,

I am having problems with the installation and the solutions proposed in the documentation didn't work so far. Your help will be really appreciated.

1st attempt: installing plastid with pip install gave me the following error:
"ERROR: Could not build wheels for plastid, which is required to install pyproject.toml-based projects"
python version: Python 3.7.10; pip version: pip version 22.0.4; Linux distribution: "CentOS Linux 7 (Core)"

2nd attempt: installing plastid in a new conda environment gave me this error:
PackagesNotFoundError: The following packages are not available from current channels:

• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/linux-64
• https://repo.anaconda.com/pkgs/r/noarch

3rd attempt: installing plastid in a vanilla environment (virtualenv) so that I make sure that there are no conflicts with other packages etc. "ERROR: Could not build wheels for plastid, which is required to install pyproject.toml-based projects"

Is there anything I am missing?? any system library or something like that? a problem with the gcc compiler?

Thank you very much in advance!

Find below the log of one of the installation attempts.

###########################################################################################
Using pip 22.0.4 from /home/lmateo/miniconda3/envs/orfrater/lib/python3.7/site-packages/pip (python 3.7)
Collecting plastid
Downloading plastid-0.6.1.tar.gz (1.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 8.5 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting pysam>=0.8.4
Downloading pysam-0.19.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.0/15.0 MB 58.4 MB/s eta 0:00:00
Collecting twobitreader>=3.0.0
Downloading twobitreader-3.1.7.tar.gz (9.2 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting biopython>=1.64
Downloading biopython-1.79-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (2.3 MB)
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Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/c0/ad/e3c052ed4e0027a8abef0a5e8441a044427d252d17d9aee06d56e62fc698/scipy-1.8.0rc1.tar.gz#sha256=54adf5c1197d6c3de2e131dc71660bb11d4e449aff79c8c231bd05dc6ad307eb (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
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Collecting scipy>=0.15.1
Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 40.1 MB/s eta 0:00:00
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Collecting pandas>=0.17.0
Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
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Collecting cython>=0.22.0
Downloading Cython-0.29.30-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 43.7 MB/s eta 0:00:00
Collecting termcolor
Downloading termcolor-1.1.0.tar.gz (3.9 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib>=1.4.0
Downloading matplotlib-3.5.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 39.1 MB/s eta 0:00:00
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Collecting numpy>=1.9.4
Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
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Collecting python-dateutil>=2.7
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
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Collecting packaging>=20.0
Downloading packaging-21.3-py3-none-any.whl (40 kB)
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Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0
Downloading fonttools-4.33.3-py3-none-any.whl (930 kB)
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Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.4.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB)
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Collecting pillow>=6.2.0
Downloading Pillow-9.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
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Collecting pyparsing>=2.2.1
Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
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Collecting pytz>=2017.3
Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB)
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Collecting typing-extensions
Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB)
Collecting six>=1.5
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: plastid, twobitreader, termcolor
Building wheel for plastid (pyproject.toml): started
Building wheel for plastid (pyproject.toml): finished with status 'error'
Building wheel for twobitreader (setup.py): started
Building wheel for twobitreader (setup.py): finished with status 'done'
Created wheel for twobitreader: filename=twobitreader-3.1.7-py3-none-any.whl size=9602 sha256=48feed40c805dbbcffafd2fcbc7731b1b7b30f4b3ee9e461f75cd207f46827ae
Stored in directory: /tmp/pip-ephem-wheel-cache-_hfd3tv8/wheels/d7/4f/70/282382e10dc13fd946f157888d9652437b01e3ac4541ac4b4b
Building wheel for termcolor (setup.py): started
Building wheel for termcolor (setup.py): finished with status 'done'
Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4848 sha256=31dede504b8826f170c8c0b1e06eb37fc09f3a70ce4b543f7beae55ea0fb5050
Stored in directory: /tmp/pip-ephem-wheel-cache-_hfd3tv8/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
Successfully built twobitreader termcolor
Failed to build plastid

[LidiaML]

I could finally install plastid using the second approach (conda). The only thing I had to do is to add the bioconda channel like this: conda config --add channels bioconda and then run conda install plastid. This might seem obvious to expert conda users but might be of help for other people ;-)

[joshuagryphon]

Glad you got this installed. I'm unsure what did not work with a non-conda install, as the install log isn't giving many clues. One possibility- plastid has some non-Python dependencies, in the form of packges and development headers zlib, libcrypto, and libssl (latter two provided by libopenssl on many Linux platforms).

I'm not a CentOS user, but if I'm not mistaken, the headers would come from these packages:

• zlib-devel
• openssl-devel

Do you have those installed on your system?

Another way to debug the system-wide install would be to generate a verbose install log to get more detail: pip install --verbose plastid