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openssl incompatibility

See original GitHub issue

% conda list | grep ssl
openssl                   1.1.1a            h14c3975_1000    conda-forge
pyopenssl                 18.0.0                   py27_0

% conda update --all
The following packages will be UPDATED:

    asn1crypto:   0.24.0-py27_0                       --> 0.24.0-py27_1003           conda-forge
    cffi:         1.11.5-py27he75722e_1               --> 1.11.5-py27h9745a5d_1001   conda-forge
    chardet:      3.0.4-py27_1                        --> 3.0.4-py27_1003            conda-forge
    conda-env:    2.6.0-1                             --> 2.6.0-1                    conda-forge
    cryptography: 2.4.2-py27h1ba5d50_0                --> 2.5-py27hb7f436b_0         conda-forge
    enum34:       1.1.6-py27_1                        --> 1.1.6-py27_1001            conda-forge
    futures:      3.2.0-py27_0                        --> 3.2.0-py27_1000            conda-forge
    idna:         2.8-py27_0                          --> 2.8-py27_1000              conda-forge
    ipaddress:    1.0.22-py27_0                       --> 1.0.22-py_1                conda-forge
    libedit:      3.1.20170329-h6b74fdf_2             --> 3.1.20170329-hf8c457e_1001 conda-forge
    libffi:       3.2.1-hd88cf55_4                    --> 3.2.1-hf484d3e_1005        conda-forge
    ncurses:      6.1-he6710b0_1                      --> 6.1-hf484d3e_1002          conda-forge
    pip:          18.1-py27_0                         --> 19.0.1-py27_0              conda-forge
    pycosat:      0.6.3-py27h14c3975_0                --> 0.6.3-py27h14c3975_1001    conda-forge
    pycparser:    2.19-py27_0                         --> 2.19-py_0                  conda-forge
    pyopenssl:    18.0.0-py27_0                       --> 19.0.0-py27_0              conda-forge
    pysocks:      1.6.8-py27_0                        --> 1.6.8-py27_1002            conda-forge
    python:       2.7.15-h9bab390_6                   --> 2.7.15-h938d71a_1006       conda-forge
    readline:     7.0-h7b6447c_5                      --> 7.0-hf8c457e_1001          conda-forge
    ruamel_yaml:  0.15.46-py27h14c3975_0              --> 0.15.71-py27h14c3975_1000  conda-forge
    setuptools:   40.6.3-py27_0                       --> 40.7.1-py27_0              conda-forge
    six:          1.12.0-py27_0                       --> 1.12.0-py27_1000           conda-forge
    sqlite:       3.26.0-h7b6447c_0                   --> 3.26.0-h67949de_1000       conda-forge
    tk:           8.6.8-hbc83047_0                    --> 8.6.9-h84994c4_1000        conda-forge
    wheel:        0.32.3-py27_0                       --> 0.32.3-py27_0              conda-forge
    yaml:         0.1.7-had09818_2                    --> 0.1.7-h14c3975_1001        conda-forge
    zlib:         1.2.11-h7b6447c_3                   --> 1.2.11-h14c3975_1004       conda-forge

The following packages will be DOWNGRADED:

    conda:        4.6.2-py27_0            conda-forge --> 4.5.12-py27_1000           conda-forge
    libgcc-ng:    8.2.0-hdf63c60_1                    --> 7.3.0-hdf63c60_0           conda-forge
    libstdcxx-ng: 8.2.0-hdf63c60_1                    --> 7.3.0-hdf63c60_0           conda-forge
    openssl:      1.1.1a-h14c3975_1000    conda-forge --> 1.0.2p-h14c3975_1002       conda-forge
    requests:     2.21.0-py27_0                       --> 2.13.0-py27_0              conda-forge
    urllib3:      1.24.1-py27_0                       --> 1.12-py27_0                bioconda

So updating causes openssl to downgrade from 1.1.1a to 1.0.2p. The problem is that those versions of openssl are binary incompatible. So all those packages that are upgraded need to be rebuilt with the latest openssl, including pyopenssl and maybe python.

This is causing endless troubles in bioconda now.

Issue Analytics

State:
Created 5 years ago
Reactions:3
Comments:20 (8 by maintainers)

Top GitHub Comments

1reaction

pb-cdunncommented, Feb 22, 2019

In ~/.condarc:

channel_priority: strict

seems to have fixed the problem. In one environment, with a particular miniconda, conda install pb-assembly tried to “upgrade” openssl to 1.1.1, but after strict, that same command did the right thing.

0reactions

pb-cdunncommented, Feb 10, 2019

I’m asking the sysadmin to install that, then I’ll try strict …

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