Certbot has problem setting up the virtual environment


#1

Hello, I tried to renew my certificate but got this error.
I need to solve it before the certificate expires, otherwise my visitors won’t be able to use my site.
It never happened before, previous renewals went smoothly without errors.
This is NOT a memory issue, as you can see:

Mem:        8167872      889812     6343700       73796      934360     6954400
Swap:       3145724           0     3145724

I have already tried the following:

  • Using --no-bootstrap
  • Reinstalling python
  • Reinstalling letsencrypt
  • Rebooting the server.

My domain is: ottavianobiella.it

I ran this command:

cd /opt/letsencrypt
sudo -H ./letsencrypt-auto certonly --webroot --renew-by-default -d ottavianobiella.it -d www.ottavianobiella.it

It produced this output:

Bootstrapping dependencies for Debian-based OSes... (you can skip this with --no                            -bootstrap)
Hit:1 http://mirrors.linode.com/ubuntu bionic InRelease
Hit:2 http://mirrors.linode.com/ubuntu bionic-updates InRelease
Get:3 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
Fetched 88.7 kB in 1s (176 kB/s)
Reading package lists... Done
Reading package lists... Done
Building dependency tree
Reading state information... Done
augeas-lenses is already the newest version (1.10.1-2).
ca-certificates is already the newest version (20180409).
libaugeas0 is already the newest version (1.10.1-2).
libffi-dev is already the newest version (3.2.1-8).
python is already the newest version (2.7.15~rc1-1).
python-dev is already the newest version (2.7.15~rc1-1).
python-virtualenv is already the newest version (15.1.0+ds-1.1).
virtualenv is already the newest version (15.1.0+ds-1.1).
libssl-dev is already the newest version (1.1.0g-2ubuntu4.3).
openssl is already the newest version (1.1.0g-2ubuntu4.3).
gcc is already the newest version (4:7.3.0-3ubuntu2.1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Creating virtual environment...
Installing Python packages...
Had a problem while installing Python packages.

pip prints the following errors:
=====================================================
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting argparse==1.4.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 11))
  Downloading https://files.pythonhosted.org/packages/f2/94/3af39d34be01a24a6e65433d19e107099374224905f1e0cc6bbe1fd22a2f/argparse-1.4.0-py2.py3-none-any.whl
Collecting pycparser==2.14 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 17))
  Downloading https://files.pythonhosted.org/packages/6d/31/666614af3db0acf377876d48688c5d334b6e493b96d21aa7d332169bee50/pycparser-2.14.tar.gz (223kB)
Collecting asn1crypto==0.22.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 21))
  Downloading https://files.pythonhosted.org/packages/97/ba/7e8117d8efcee589f4d96dd2b2eb1d997f96d27d214cf2b7134ad8acf6ab/asn1crypto-0.22.0-py2.py3-none-any.whl (97kB)
Collecting cffi==1.11.5 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 24))
  Downloading https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl (407kB)
Collecting ConfigArgParse==0.12.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 57))
  Downloading https://files.pythonhosted.org/packages/17/8d/4a41f11b0971017c7001f118be8003da8f7b96b010c66cd792b76658d1e1/ConfigArgParse-0.12.0.tar.gz (41kB)
Collecting configobj==5.0.6 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 60))
  Downloading https://files.pythonhosted.org/packages/64/61/079eb60459c44929e684fa7d9e2fdca403f67d64dd9dbac27296be2e0fab/configobj-5.0.6.tar.gz
Collecting cryptography==2.2.2 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 63))
  Downloading https://files.pythonhosted.org/packages/dd/c2/3a5bfefb25690725824ade71e6b65449f0a9f4b29702cce10560f786ebf6/cryptography-2.2.2-cp27-cp27mu-manylinux1_x86_64.whl (2.2MB)
Collecting enum34==1.1.2 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 83))
  Downloading https://files.pythonhosted.org/packages/6f/e9/08fd439384b7e3d613e75a6c8236b8e64d90c47d23413493b38d4229a9a5/enum34-1.1.2.tar.gz (46kB)
Collecting funcsigs==1.0.2 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 86))
  Downloading https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting idna==2.5 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 89))
  Downloading https://files.pythonhosted.org/packages/11/7d/9bbbd7bb35f34b0169542487d2a8859e44306bb2e6a4455d491800a5621f/idna-2.5-py2.py3-none-any.whl (55kB)
Collecting ipaddress==1.0.16 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 92))
  Downloading https://files.pythonhosted.org/packages/23/6a/813ac29a01e4c33c19c2bded98ac3d4266ebbf0bd2c0eb0020e1c969958d/ipaddress-1.0.16-py27-none-any.whl
Collecting josepy==1.1.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 95))
  Downloading https://files.pythonhosted.org/packages/23/46/30ac29742b03be92e05d1fd9048df6f0902bb0b3b042a7ea76a2b3c30f7e/josepy-1.1.0-py2.py3-none-any.whl (53kB)
Collecting linecache2==1.0.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 98))
  Downloading https://files.pythonhosted.org/packages/c7/a3/c5da2a44c85bfbb6eebcfc1dde24933f8704441b98fdde6528f4831757a6/linecache2-1.0.0-py2.py3-none-any.whl
Collecting mock==1.3.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 102))
  Downloading https://files.pythonhosted.org/packages/b2/50/664a70b87408bb6c14c1af2337efa64eb8d1af80c933531758b8fb41ec25/mock-1.3.0-py2.py3-none-any.whl (56kB)
Collecting ordereddict==1.1 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 105))
  Downloading https://files.pythonhosted.org/packages/53/25/ef88e8e45db141faa9598fbf7ad0062df8f50f881a36ed6a0073e1572126/ordereddict-1.1.tar.gz
Collecting packaging==16.8 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 108))
  Downloading https://files.pythonhosted.org/packages/87/1b/c39b7c65b5612812b83d6cab7ef2885eac9f6beb0b7b8a7071a186aea3b1/packaging-16.8-py2.py3-none-any.whl
Collecting parsedatetime==2.1 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 111))
  Downloading https://files.pythonhosted.org/packages/85/1f/13fc06097e516f6259d62cea502b116451321c96e18a9d0fff9da3442e02/parsedatetime-2.1-py2-none-any.whl
Collecting pbr==1.8.1 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 114))
  Downloading https://files.pythonhosted.org/packages/fc/37/94af8387babb09796d306b18cf94ee5c70388c875a16d8a88e471500452c/pbr-1.8.1-py2.py3-none-any.whl (89kB)
Collecting pyOpenSSL==16.2.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 117))
  Downloading https://files.pythonhosted.org/packages/ac/93/b4cd538d31adacd07f83013860db6b88d78755af1f3fefe68ec22d397e7b/pyOpenSSL-16.2.0-py2.py3-none-any.whl (43kB)
Collecting pyparsing==2.1.8 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 120))
  Downloading https://files.pythonhosted.org/packages/85/b9/188515f35f78533b3f82966a2c3f1a71a86df8b801367ee75a77191a861d/pyparsing-2.1.8-py2.py3-none-any.whl (54kB)
Collecting pyRFC3339==1.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 129))
  Downloading https://files.pythonhosted.org/packages/9b/0a/decfa17e7707afca17d6e9595ff5c79c1c71c74063ad95576f897ed3a9f1/pyRFC3339-1.0-py2.py3-none-any.whl
Collecting python-augeas==0.5.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 132))
  Downloading https://files.pythonhosted.org/packages/41/e6/4b6740cb3e31b82252099994cea751c648b846aa7874343c31d68c2215be/python-augeas-0.5.0.tar.gz (90kB)
Collecting pytz==2015.7 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 135))
  Downloading https://files.pythonhosted.org/packages/c0/28/973f0382c803b21734cd7e97e0590928148ee21b1cbe8f7fed8b506204fb/pytz-2015.7-py2.py3-none-any.whl (476kB)
Collecting requests==2.20.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 149))
  Downloading https://files.pythonhosted.org/packages/f1/ca/10332a30cb25b627192b4ea272c351bce3ca1091e541245cccbace6051d8/requests-2.20.0-py2.py3-none-any.whl (60kB)
Collecting six==1.10.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 152))
  Downloading https://files.pythonhosted.org/packages/c8/0a/b6723e1bc4c516cb687841499455a8505b44607ab535be01091c0f24f079/six-1.10.0-py2.py3-none-any.whl
Collecting traceback2==1.4.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 155))
  Downloading https://files.pythonhosted.org/packages/17/0a/6ac05a3723017a967193456a2efa0aa9ac4b51456891af1e2353bb9de21e/traceback2-1.4.0-py2.py3-none-any.whl
Collecting unittest2==1.1.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 158))
  Downloading https://files.pythonhosted.org/packages/72/20/7f0f433060a962200b7272b8c12ba90ef5b903e218174301d0abfd523813/unittest2-1.1.0-py2.py3-none-any.whl (96kB)
Collecting zope.component==4.2.2 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 161))
  Downloading https://files.pythonhosted.org/packages/4c/c4/3f77127c876f49af478e8ea4dc223cda17730bb273c0d1606a4114c64008/zope.component-4.2.2.tar.gz (546kB)
Collecting zope.event==4.1.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 164))
  Downloading https://files.pythonhosted.org/packages/0e/87/75e3d62a3506953c2e56d15a150de31e5d92310e87db2c8b102dc01b0b8e/zope.event-4.1.0.tar.gz (476kB)
Collecting zope.interface==4.1.3 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 167))
  Downloading https://files.pythonhosted.org/packages/9d/81/2509ca3c6f59080123c1a8a97125eb48414022618cec0e64eb1313727bfe/zope.interface-4.1.3.tar.gz (141kB)
Collecting requests-toolbelt==0.8.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 185))
  Downloading https://files.pythonhosted.org/packages/97/8a/d710f792d6f6ecc089c5e55b66e66c3f2f35516a1ede5a8f54c13350ffb0/requests_toolbelt-0.8.0-py2.py3-none-any.whl (54kB)
Collecting chardet==3.0.2 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 188))
  Downloading https://files.pythonhosted.org/packages/b8/74/54fdc2fcfdd46b6c486964b64c5bb7db9a3664033ab25cf11aab06dd2a5d/chardet-3.0.2-py2.py3-none-any.whl (133kB)
Collecting urllib3==1.24.1 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 191))
  Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB)
Collecting certifi==2017.4.17 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 194))
  Downloading https://files.pythonhosted.org/packages/eb/01/c1f58987b777d6c4ec535b4e004a4a07bfc9db06f0c7533367ca6da8f2a6/certifi-2017.4.17-py2.py3-none-any.whl (375kB)
Collecting letsencrypt==0.7.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 205))
  Downloading https://files.pythonhosted.org/packages/fd/21/0c6f33829fadec8aca0c1ebb4d6f8101c05899356a58d1b2e506cb77cf18/letsencrypt-0.7.0-py2-none-any.whl
Collecting certbot==0.30.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 209))
  Downloading https://files.pythonhosted.org/packages/e0/5e/9881564f386c1294d6cf387d5c754d7eb3277507b46afac1c646d6ae6de6/certbot-0.30.0-py2.py3-none-any.whl (317kB)
Collecting acme==0.30.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 212))
  Downloading https://files.pythonhosted.org/packages/df/a7/fc6114c715233ab53c9571d3b710d596bc80446eac14e0906362fa69e4b1/acme-0.30.0-py2.py3-none-any.whl (85kB)
Collecting certbot-apache==0.30.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 215))
  Downloading https://files.pythonhosted.org/packages/37/37/46433ff4358e12d1caf4101308411bf1dad0df3e27e2e62c5037ca75d2e0/certbot_apache-0.30.0-py2.py3-none-any.whl (228kB)
Collecting certbot-nginx==0.30.0 (from -r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 218))
  Downloading https://files.pythonhosted.org/packages/ad/15/7f42f31ba068f837816647135a0704a8c89aad685df160407e92870c0277/certbot_nginx-0.30.0-py2.py3-none-any.whl (90kB)
Requirement already satisfied: setuptools>=1.0 in /opt/eff.org/certbot/venv/lib/python2.7/site-packages (from josepy==1.1.0->-r /tmp/tmp.GipM6EYHNW/letsencrypt-auto-requirements.txt (line 95)) (40.6.3)
Installing collected packages: argparse, pycparser, asn1crypto, cffi, ConfigArgParse, six, configobj, enum34, idna, ipaddress, cryptography, funcsigs, pyOpenSSL, josepy, linecache2, pbr, mock, ordereddict, pyparsing, packaging, parsedatetime, pytz, pyRFC3339, python-augeas, urllib3, certifi, chardet, requests, traceback2, unittest2, zope.interface, zope.event, zope.component, requests-toolbelt, acme, certbot, letsencrypt, certbot-apache, certbot-nginx
  Found existing installation: argparse 1.2.1
    Not uninstalling argparse at /usr/lib/python2.7, outside environment /opt/eff.org/certbot/venv
    Can't uninstall 'argparse'. No files were found to uninstall.
  Running setup.py install for pycparser: started
    Running setup.py install for pycparser: finished with status 'done'
  Running setup.py install for ConfigArgParse: started
    Running setup.py install for ConfigArgParse: finished with status 'done'
  Running setup.py install for configobj: started
    Running setup.py install for configobj: finished with status 'done'
  Running setup.py install for enum34: started
    Running setup.py install for enum34: finished with status 'done'
  Running setup.py install for ordereddict: started
    Running setup.py install for ordereddict: finished with status 'done'
  Running setup.py install for python-augeas: started
    Running setup.py install for python-augeas: finished with status 'done'
  Running setup.py install for zope.interface: started
    Running setup.py install for zope.interface: finished with status 'done'
  Running setup.py install for zope.event: started
    Running setup.py install for zope.event: finished with status 'done'
  Running setup.py install for zope.component: started
    Running setup.py install for zope.component: finished with status 'done'
Exception:
Traceback (most recent call last):
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py", line 176, in main
    status = self.run(options, args)
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 393, in run
    use_user_site=options.use_user_site,
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 57, in install_given_reqs
    **kwargs
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 919, in install
    use_user_site=use_user_site, pycompile=pycompile,
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 445, in move_wheel_files
    warn_script_location=warn_script_location,
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/wheel.py", line 583, in move_wheel_files
    outrows = get_csv_rows_for_installed(reader)
  File "/opt/eff.org/certbot/venv/local/lib/python2.7/site-packages/pip/_internal/wheel.py", line 565, in get_csv_rows_for_installed
    for fpath, digest, length in old_csv_rows:
ValueError: too many values to unpack
=====================================================

Certbot has problem setting up the virtual environment.

We were not be able to guess the right solution from your pip
output.

Consult https://certbot.eff.org/docs/install.html#problems-with-python-virtual-environment
for possible solutions.
You may also find some support resources at https://certbot.eff.org/support/ .

My web server is (include version): Apache 2.4.9

The operating system my web server runs on is (include version): Ubuntu 18.0.4.1

My hosting provider, if applicable, is: Linode

I can login to a root shell on my machine (yes or no, or I don’t know): yes

I’m using a control panel to manage my site (no, or provide the name and version of the control panel): no

The version of my client is (e.g. output of certbot --version or certbot-auto --version if you’re using Certbot): 0.23.0


#2

Hi @otpabu

please read


#3

That’s a different bug which has been fixed. :confounded:


#4

Thank you. I tried this solution, run the command again, and it worked.

sudo sed -i 's/virtualenv --no-site-packages/virtualenv --no-download --no-site-packages/' /opt/letsencrypt/certbot-auto


#5

For posterity:


#6

I too am getting the same error. @otpabu solution had no effect for me


#7

Seems to be missing the -w parameter (and associated path).
[not related to this problem but may cause another problem later]


closed #8

This topic was automatically closed 30 days after the last reply. New replies are no longer allowed.