Conda 4.5.11/Linux-64 SSLError(SSLError("Can't connect to HTTPS URL because the SSL module is not available.",),)

[nkuehnle]

Current Behavior

I'm having issues installing anything using the conda install command. I've been looking around for solutions but a lot are deep into some Windows 10 discussion. The things I can find that are specific to Linux-64 haven't worked (set ssl_very: false, then try to update/install packages, including: openssl ca-certificates certifi.

Steps to Reproduce

This is representative of every conda isntall command.

$ conda install -c conda-forge -c bioconda samtools bzip2
Solving environment: failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/linux-64/repodata.json.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

If your current network has https://www.anaconda.com blocked, please file
a support request with your network engineering team.

SSLError(SSLError("Can't connect to HTTPS URL because the SSL module is not available.",),)

Expected Behavior

Should install the requested package. conda update is also misbehaving.

conda update openssl ca-certificates certifi

PackageNotInstalledError: Package is not installed in prefix.
  prefix: /home/user/anaconda3
  package name: certifi

Maybe has something to do with certifi package? Attempting to install that package using conda install gives the same error gives the same error as any other.

Environment Information

conda info

     active environment : None
            shell level : 0
       user config file : /home/user/.condarc
 populated config files : /home/user/.condarc
          conda version : 4.5.11
    conda-build version : 2.0.6
         python version : 3.5.2.final.0
       base environment : /home/user/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/user/anaconda3/pkgs
                          /home/user/.conda/pkgs
       envs directories : /home/user/anaconda3/envs
                          /home/user/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.13.0 CPython/3.5.2 Linux/2.6.32-573.7.1.el6.x86_64 centos/6.10 glibc/2.12
                UID:GID : 500:500
             netrc file : None
           offline mode : False

conda config --show

add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
  - ca-certificates
  - certifi
  - openssl
allow_non_channel_urls: False
allow_softlinks: False
always_copy: False
always_softlink: False
always_yes: None
anaconda_upload: None
auto_update_conda: True
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
  - bioconda
  - r
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
create_default_packages: []
custom_channels:
  pkgs/r: https://repo.anaconda.com
  pkgs/pro: https://repo.anaconda.com
  pkgs/free: https://repo.anaconda.com
  pkgs/main: https://repo.anaconda.com
custom_multichannels:
  defaults: ["https://repo.anaconda.com/pkgs/main", "https://repo.anaconda.com/pkgs/free", "https://repo.anaconda.com/pkgs/r", "https://repo.anaconda.com/pkgs/pro"]
  local: []
default_channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/free
  - https://repo.anaconda.com/pkgs/r
  - https://repo.anaconda.com/pkgs/pro
disallowed_packages: []
download_only: False
envs_dirs:
  - /home/user/anaconda3/envs
  - /home/user/.conda/envs
force: False
json: False
local_repodata_ttl: 1
max_shlvl: 2
migrated_channel_aliases: []
no_dependencies: False
non_admin_enabled: True
notify_outdated_conda: True
offline: False
override_channels_enabled: True
path_conflict: clobber
pinned_packages: []
pkgs_dirs:
  - /home/user/anaconda3/pkgs
  - /home/user/.conda/pkgs
proxy_servers: {}
quiet: False
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
report_errors: None
rollback_enabled: True
safety_checks: warn
shortcuts: True
show_channel_urls: None
ssl_verify: False
track_features: []
use_index_cache: False
use_pip: True
verbosity: 0
whitelist_channels: []

conda list

# packages in environment at /home/user/anaconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_nb_ext_conf              0.3.0                    py35_0  
abstract-rendering        0.5.1               np111py35_0  
alabaster                 0.7.9                    py35_0  
anaconda                  custom                   py35_0  
anaconda-client           1.5.2                    py35_0  
appdirs                   1.4.0                    py35_0    bioconda
argcomplete               1.0.0                    py35_1  
astropy                   1.2.1               np111py35_0  
babel                     2.3.4                    py35_0  
beautifulsoup4            4.5.1                    py35_0  
bioconductor-annotate     1.50.0                 r3.3.1_1    bioconda
bioconductor-annotationdbi 1.34.4                 r3.3.1_1    bioconda
bioconductor-biobase      2.32.0                 r3.3.1_0    bioconda
bioconductor-biocgenerics 0.18.0                 r3.3.1_0    bioconda
bioconductor-genefilter   1.54.2                 r3.3.1_0    bioconda
bioconductor-iranges      2.6.1                  r3.3.1_0    bioconda
bioconductor-s4vectors    0.10.3                 r3.3.1_0    bioconda
bioconductor-sva          3.18.0                        0    bioconda
bitarray                  0.8.1                    py35_0  
blaze-core                0.9.0                    py35_0  
bokeh                     0.12.3                   py35_0  
boto                      2.42.0                   py35_0  
bzip2                     1.0.6                         3  
ca-certificates           2020.1.1                      0  
cairo                     1.12.18                       6  
cffi                      1.8.3                    py35_0  
click                     6.6                      py35_0    bioconda
clyent                    1.2.2                    py35_0  
colorama                  0.3.7                    py35_0  
conda                     4.5.11                   py35_0  
conda-build               2.0.6                    py35_0  
conda-env                 2.6.0                         1  
configobj                 5.0.6                    py35_0  
cryptography              1.5.2                    py35_0  
curl                      7.62.0               hbc83047_0  
cutadapt                  1.11                     py35_0    bioconda
cycler                    0.10.0                   py35_0  
cython                    0.24.1                   py35_0  
cytoolz                   0.8.0                    py35_0  
datashape                 0.5.2                    py35_0  
decorator                 4.0.10                   py35_0  
docutils                  0.12                     py35_2  
dropbox                   5.2.1                    py35_0    bioconda
ecdsa                     0.13                     py35_0  
entrypoints               0.2.2                    py35_0  
et_xmlfile                1.0.1                    py35_0  
fastcache                 1.0.2                    py35_1  
fastqc                    0.11.5                        1    bioconda
filechunkio               1.6                      py35_0    bioconda
filelock                  2.0.6                    py35_0  
flask                     0.11.1                   py35_0  
fontconfig                2.11.1                        6  
freetype                  2.5.5                         1  
ftputil                   3.2                      py35_0    bioconda
glib                      2.43.0                        2    r
greenlet                  0.4.10                   py35_0  
gsl                       1.16                          1    r
h5py                      2.6.0               np111py35_2  
harfbuzz                  0.9.35                        6    r
hdf5                      1.8.17                        1  
htslib                    1.9                  h4da6232_3    bioconda
icu                       54.1                          0  
idna                      2.1                      py35_0  
imagesize                 0.7.1                    py35_0  
ipykernel                 4.5.0                    py35_0  
ipython                   5.1.0                    py35_0  
ipython-notebook          4.0.4                    py35_0  
ipython-qtconsole         4.0.1                    py35_0  
ipython_genutils          0.1.0                    py35_0  
ipywidgets                5.2.2                    py35_0  
itsdangerous              0.24                     py35_0  
java-jdk                  8.0.92                        1    bioconda
jbig                      2.1                           0  
jdcal                     1.3                      py35_0  
jedi                      0.9.0                    py35_1  
jinja2                    2.8                      py35_1  
jpeg                      8d                            2  
jsonschema                2.5.1                    py35_0  
jupyter                   1.0.0                    py35_3  
jupyter_client            4.4.0                    py35_0  
jupyter_console           5.0.0                    py35_0  
jupyter_core              4.2.0                    py35_0  
libcurl                   7.62.0               h20c2e04_0  
libdeflate                1.2                  h516909a_1    bioconda
libffi                    3.2.1                         0  
libgcc                    4.8.5                         1    r
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran               3.0.0                         1  
libpng                    1.6.22                        0  
libsodium                 1.0.10                        0  
libssh2                   1.9.0                h1ba5d50_1  
libstdcxx-ng              8.2.0                hdf63c60_1  
libtiff                   4.0.6                         2  
libxml2                   2.9.3                         0    bioconda
libxslt                   1.1.28                        0  
lxml                      3.6.4                    py35_0  
mageck                    0.5.2                     <pip>
mageck                    0.5.7                    py35_4    bioconda
markupsafe                0.23                     py35_2  
matplotlib                1.5.1               np111py35_0  
mistune                   0.7.3                    py35_0  
mkl                       11.3.3                        0  
mkl-service               1.1.2                    py35_2  
mpmath                    0.19                     py35_1  
multipledispatch          0.4.9                    py35_0  
nb_anacondacloud          1.2.0                    py35_0  
nb_conda                  2.0.0                    py35_0  
nb_conda_kernels          2.0.0                    py35_0  
nbconvert                 4.2.0                    py35_0  
nbformat                  4.1.0                    py35_0  
nbpresent                 3.0.2                    py35_0  
ncurses                   6.1                  he6710b0_1  
networkx                  1.11                     py35_0  
nltk                      3.2.1                    py35_0  
nose                      1.3.7                    py35_1  
notebook                  4.2.3                    py35_0  
numexpr                   2.6.1               np111py35_0  
numpy                     1.11.2                   py35_0  
odo                       0.5.0                    py35_1  
openblas                  0.2.14                        4  
openpyxl                  2.4.0                    py35_0    bioconda
openssl                   1.1.1f               h7b6447c_0  
pandas                    0.19.0              np111py35_0  
pango                     1.36.8                        3    r
paramiko                  2.0.2                    py35_0  
patchelf                  0.9                           0  
path.py                   8.2.1                    py35_0  
patsy                     0.4.1                    py35_0  
pcre                      8.39                          0  
pep8                      1.7.0                    py35_0  
pexpect                   4.0.1                    py35_0  
pickleshare               0.7.4                    py35_0  
pillow                    3.4.2                    py35_0  
pip                       8.1.2                    py35_0  
pixman                    0.32.6                        0  
pkginfo                   1.3.2                    py35_0  
ply                       3.9                      py35_0  
prompt_toolkit            1.0.3                    py35_0  
psutil                    4.4.0                    py35_0  
ptyprocess                0.5.1                    py35_0  
py                        1.4.31                   py35_0  
pyasn1                    0.1.9                    py35_0  
pycosat                   0.6.3            py35h14c3975_0  
pycparser                 2.16                     py35_0  
pycrypto                  2.6.1                    py35_4  
pycurl                    7.43.0.2         py35hb7f436b_0  
pyflakes                  1.3.0                    py35_0  
pygments                  2.1.3                    py35_0  
pyopenssl                 16.2.0                   py35_0  
pyparsing                 2.1.4                    py35_0  
pyqt                      4.11.4                   py35_4  
pysftp                    0.2.8                    py35_0    bioconda
pytables                  3.2.3.1             np111py35_0  
pytest                    3.0.3                    py35_0  
python                    3.5.2                         0  
python-dateutil           2.3                      py35_0    bioconda
pytz                      2016.7                   py35_0  
pyyaml                    3.12                     py35_0  
pyzmq                     16.0.0                   py35_0  
qt                        4.8.7                         4  
qtconsole                 4.2.1                    py35_0  
r                         3.3.1                  r3.3.1_0    r
r-base                    3.3.1                         3    r
r-boot                    1.3_18                 r3.3.1_0    r
r-class                   7.3_14                 r3.3.1_0    r
r-cluster                 2.0.4                  r3.3.1_0    r
r-codetools               0.2_14                 r3.3.1_0    r
r-dbi                     0.4_1                  r3.3.1_0    r
r-foreign                 0.8_66                 r3.3.1_0    r
r-kernsmooth              2.23_15                r3.3.1_0    r
r-lattice                 0.20_33                r3.3.1_0    r
r-mass                    7.3_45                 r3.3.1_0    r
r-matrix                  1.2_6                  r3.3.1_0    r
r-mgcv                    1.8_12                 r3.3.1_0    r
r-nlme                    3.1_128                r3.3.1_0    r
r-nnet                    7.3_12                 r3.3.1_0    r
r-recommended             3.3.1                  r3.3.1_0    r
r-rpart                   4.1_10                 r3.3.1_0    r
r-rsqlite                 1.0.0                  r3.3.1_2    r
r-spatial                 7.3_11                 r3.3.1_0    r
r-survival                2.39_4                 r3.3.1_0    r
r-xml                     3.98_1.4               r3.3.1_0    r
r-xtable                  1.8_2                  r3.3.1_0    r
readline                  6.2                           2  
redis                     3.2.0                         0  
redis-py                  2.10.5                   py35_0  
requests                  2.13.0                   py35_0  
rope                      0.9.4                    py35_1  
rpy2                      2.7.8              py35r3.3.1_1    bioconda
ruamel_yaml               0.11.14                  py35_0  
samtools                  1.9                 h10a08f8_12    bioconda
scikit-image              0.12.3              np111py35_1  
scikit-learn              0.18                np111py35_0  
scipy                     0.18.1              np111py35_0  
setuptools                27.2.0                   py35_0  
simplegeneric             0.8.1                    py35_1  
sip                       4.18                     py35_0  
six                       1.10.0                   py35_0  
snakemake                 3.8.2                    py35_0    bioconda
snowballstemmer           1.2.1                    py35_0  
sockjs-tornado            1.0.3                    py35_0  
sphinx                    1.4.8                    py35_0  
sphinx_rtd_theme          0.1.9                    py35_0  
spyder                    2.3.8                    py35_1  
spyder-app                2.3.8                    py35_0  
sqlalchemy                1.1.2                    py35_0  
sqlite                    3.13.0                        0  
statsmodels               0.6.1               np111py35_1  
sympy                     1.0                      py35_0  
terminado                 0.6                      py35_0  
theano                    0.8.2                    py35_0  
tk                        8.5.18                        0  
toolz                     0.8.0                    py35_0  
tornado                   4.4.2                    py35_0  
traitlets                 4.3.1                    py35_0  
ujson                     1.35                     py35_0  
unicodecsv                0.14.1                   py35_0  
urllib3                   1.12                     py35_0    bioconda
util-linux                2.21                          0  
vispr                     0.4.13                   py35_0    bioconda
wcwidth                   0.1.7                    py35_0  
werkzeug                  0.11.11                  py35_0  
wheel                     0.29.0                   py35_0  
widgetsnbextension        1.2.6                    py35_0  
wrapt                     1.10.8                   py35_0  
xlrd                      1.0.0                    py35_0  
xlsxwriter                0.9.3                    py35_0  
xlwt                      1.1.2                    py35_0  
xz                        5.2.4                h14c3975_4  
yaml                      0.1.6                         0  
zeromq                    4.1.5                         0  
zlib                      1.2.11               h7b6447c_3  

[chenghlee]

Are you still having this problem? If so, one possibility is that your version of the requests package is really old.

[nkuehnle]

Are you still having this problem? If so, one possibility is that your version of the requests package is really old.

Yeah, I have a small workaround in that I dual-booted my home desktop w/ Ubuntu and did a fresh install of anaconda and the packages I personally need to use and things are running nicely there.

I'm thinking a fresh install might be easiest here. Our workstation at work hasn't been updated in any form for a few years now. I think the person who had been operating it for the past several years was avoiding it because the mageck package seems like it probably has to be installed in an insulated environment working from newer versions of anaconda and they simply did not want to do that.

If there is a way I can update only the requests package, that might be easiest (I'm assuming I'd need to manually install it?). I wouldn't mind preserving our current set of packages, although tbh even that seems quite unwieldly to me and I'm not sure we'll need to use most of them. It's been years since I used linux and I'm still pretty fresh to Python, but I think I can probably get most of them up and running if I need to again.

[veronic]

I have same problem and I do not know how to solve it.
It's been a year. Do you have a solution？

[github-actions]

Hi there, thank you for your contribution!

This issue has been automatically marked as stale because it has not had recent activity. It will be closed automatically if no further activity occurs.

If you would like this issue to remain open please:

1. Verify that you can still reproduce the issue at hand
2. Comment that the issue is still reproducible and include:
   - What OS and version you reproduced the issue on
   - What steps you followed to reproduce the issue

NOTE: If this issue was closed prematurely, please leave a comment.

Thanks!

[github-actions]

Hi again!

This issue has been closed since it has not had recent activity.

NOTE: If this issue was closed prematurely, please leave a comment.

Thanks!