Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Not all site-packages available when installed with --site-packages #3718

vlad0337187 opened this issue Apr 29, 2019 · 8 comments · Fixed by #3836

Not all site-packages available when installed with --site-packages #3718

vlad0337187 opened this issue Apr 29, 2019 · 8 comments · Fixed by #3836
Priority: Medium Status: Needs More Information Type: Discussion Type: Possible Bug


Copy link

@vlad0337187 vlad0337187 commented Apr 29, 2019

Issue description

If to create env with '--site-packages' option, no system packages are available in environment.

Expected result

System packages available in virtual environment.

Actual result

No system packages are available in virtualenv.
In system I have installed xdg package (from apt python3-xdg), it's placed in /usr/lib/python3/dist-packages/xdg.
I can import it from system python.
Can't import it from python inside pipenv environment.

python3.6 -m site in system:

sys.path = [
USER_BASE: '/home/vlad/.local' (exists)
USER_SITE: '/home/vlad/.local/lib/python3.6/site-packages' (exists)

python -m site in pipenv virtualenv:

sys.path = [
USER_BASE: '/home/vlad/.local' (exists)
USER_SITE: '/home/vlad/.local/lib/python3.6/site-packages' (exists)

System: Mint 19.1 (Ubuntu 16.04).
Used Python: 3.6 (system default)

Steps to replicate

pipenv --site-packages install
pipenv shell
import xdg # will throw import error. Same in sytem won't

Please run $ pipenv --support, and paste the results here. Don't put backticks (`) around it! The output already contains Markdown formatting.

Can't run the following (xclip not installed), so runned it without xclip:

$ pipenv --support | xclip
$ pipenv --support

Pipenv version: '2018.11.26'

Pipenv location: '/home/vlad/.local/lib/python3.6/site-packages/pipenv'

Python location: '/usr/bin/python3'

Python installations found:

  • 3.7.3: /usr/bin/python3.7
  • 3.7.3: /usr/bin/python3.7m
  • 3.6.7: /home/vlad/.local/share/virtualenvs/gtg-cnQmc6C0/bin/python3
  • 3.6.7: /usr/bin/python3.6
  • 3.6.7: /usr/bin/python3.6m
  • 3.5.3: /home/vlad/.local/bin/pypy3
  • 2.7.15rc1: /usr/bin/python

PEP 508 Information:

{'implementation_name': 'cpython',
 'implementation_version': '3.6.7',
 'os_name': 'posix',
 'platform_machine': 'x86_64',
 'platform_python_implementation': 'CPython',
 'platform_release': '4.15.0-47-generic',
 'platform_system': 'Linux',
 'platform_version': '#50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019',
 'python_full_version': '3.6.7',
 'python_version': '3.6',
 'sys_platform': 'linux'}

System environment variables:

  • LANG
  • USER
  • PWD
  • HOME
  • TERM
  • PATH
  • PS1
  • _

Pipenv–specific environment variables:


Debug–specific environment variables:

  • PATH: /home/vlad/.local/share/virtualenvs/gtg-cnQmc6C0/bin:/home/vlad/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/vlad/.local/bin:/home/vlad/.local/bin
  • SHELL: /bin/bash
  • LANG: en_US.UTF-8
  • PWD: /home/vlad/Programs/organizing/gtg
  • VIRTUAL_ENV: /home/vlad/.local/share/virtualenvs/gtg-cnQmc6C0

Contents of Pipfile ('/home/vlad/Programs/organizing/gtg/Pipfile'):

name = "pypi"
url = ""
verify_ssl = true


nose = "*"
spec = "*"
pyflakes = "*"
pep8 = "*"
mock = "*"
liblarch = {git = "",ref = "master"}

python_version = "3.6"

dev = './'

Contents of Pipfile.lock ('/home/vlad/Programs/organizing/gtg/Pipfile.lock'):

    "_meta": {
        "hash": {
            "sha256": "1b305c19130f0cd80840f0090f3dcd67442c476c71f5bf53e27fc7a35fe4c0d2"
        "pipfile-spec": 6,
        "requires": {
            "python_version": "3.6"
        "sources": [
                "name": "pypi",
                "url": "",
                "verify_ssl": true
    "default": {
        "liblarch": {
            "git": "",
            "ref": "ebd05dde26ce8dce2ab181d78bab64750e84a04c"
        "mock": {
            "hashes": [
            "index": "pypi",
            "version": "==2.0.0"
        "nose": {
            "hashes": [
            "index": "pypi",
            "version": "==1.3.7"
        "pbr": {
            "hashes": [
            "version": "==5.2.0"
        "pep8": {
            "hashes": [
            "index": "pypi",
            "version": "==1.7.1"
        "pyflakes": {
            "hashes": [
            "index": "pypi",
            "version": "==2.1.1"
        "six": {
            "hashes": [
            "version": "==1.12.0"
        "spec": {
            "hashes": [
            "index": "pypi",
            "version": "==1.4.1"
    "develop": {}

P.S. also add pipenv --site-packages install output.
Now It's python3.6.7 instead of python3.6.6 in my system, but bug is still present.

pipenv --site-packages install pipenv --site-packages install Creating a virtualenv for this project… Pipfile: /home/vlad/Desktop/temp/testing/test_venv/Pipfile Using /usr/bin/python3.6 (3.6.7) to create virtualenv… ⠋ Creating virtual environment...Using base prefix '/usr' New python executable in /home/vlad/.local/share/virtualenvs/test_venv-Omu8UKuC/bin/python3.6 Also creating executable in /home/vlad/.local/share/virtualenvs/test_venv-Omu8UKuC/bin/python Installing setuptools, pip, wheel...done. Running virtualenv with interpreter /usr/bin/python3.6

Successfully created virtual environment!
Virtualenv location: /home/vlad/.local/share/virtualenvs/test_venv-Omu8UKuC
Installing dependencies from Pipfile.lock (8c4c43)…
🐍 ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 10/10 — 00:00:15
To activate this project's virtualenv, run pipenv shell.
Alternatively, run a command inside the virtualenv with pipenv run.

Copy link

@jxltom jxltom commented May 9, 2019

Which python path are you using to create virtualenv by pipenv --site-packages install? Could you output the content such as Using /Users/username/.pyenv/versions/3.6.6/bin/python3.6 (3.6.6) to create virtualenv...?

@jxltom jxltom added the Status: Awaiting Update label May 9, 2019
Copy link

@Marviel Marviel commented May 10, 2019

I had this same issue some months ago and my only strategy was to pin an old pipenv version. I really hope this can be fixed soon, because the new versions of Pipenv have a lot to offer :/


^^^ That issue includes a dockerized reproducibility case.

Copy link

@vlad0337187 vlad0337187 commented May 16, 2019

@jxltom , I used python3.6 for that (the only version except 2.7 in my system).
Added info you asked to my first message (to the end).

Checked, bug is still present.

@jxltom jxltom removed the Status: Awaiting Update label May 17, 2019
Copy link

@jxltom jxltom commented May 17, 2019

Thanks for the additional info!

Copy link

@techalchemy techalchemy commented May 20, 2019

Yeah we are consciously disabling user site access although I'm not sure why that is carrying into virtualenvs... I can't actually remember the reason why we needed to disable user site permission, but I believe it involved something about setuptools and editable installs...

@techalchemy techalchemy added Priority: Medium Status: Needs More Information Type: Discussion Type: Possible Bug labels May 20, 2019
@techalchemy techalchemy self-assigned this May 20, 2019
Copy link

@vlad0337187 vlad0337187 commented May 30, 2019

For me it should help accessing packages, which can't be installed in virtualenv.
For example, when developing GTK cross-distributive apps.
I always use system libraries, just make Python code working with them all.

Now what I did - I found virtualenv created by pipenv, made many soft links to directories for system packages, which is too long way - I should repeat it for every distributive I test app.

So, hope, it could be fixed.
Accessing to system packages, while also installed in virtualenv - helps to work in a more comfortable way.

techalchemy added a commit that referenced this issue Jul 11, 2019
- Sometimes we fail to respect `--site-packages` when it is passed with
- This resolves that and ensures we always pass it to `ensure_project`
- Fixes #3718

Signed-off-by: Dan Ryan <>
Copy link

@frostming frostming commented Jul 11, 2019

Can you try against the master branch to confirm if it still exists?

Copy link

@scresante scresante commented Jul 14, 2019

@frostming I just tried with master and the issue is resolved for me.

Any idea when the next release will be?

fwojciak pushed a commit to fwojciak/pipenv that referenced this issue May 29, 2020
2020.5.28 (2020-05-28)

Features & Improvements

-   `pipenv install` and `pipenv sync` will no longer attempt to install satisfied dependencies during installation. pypa#3057, pypa#3506
-   Added support for resolution of direct-url dependencies in `` files to respect `PEP-508` style URL dependencies. pypa#3148
-   Added full support for resolution of all dependency types including direct URLs, zip archives, tarballs, etc.
    -   Improved error handling and formatting.
    -   Introduced improved cross platform stream wrappers for better `stdout` and `stderr` consistency. pypa#3298
-   For consistency with other commands and the `--dev` option description, `pipenv lock --requirements --dev` now emits both default and development dependencies. The new `--dev-only` option requests the previous behaviour (e.g. to generate a `dev-requirements.txt` file). pypa#3316
-   Pipenv will now successfully recursively lock VCS sub-dependencies. pypa#3328
-   Added support for `--verbose` output to `pipenv run`. pypa#3348
-   Pipenv will now discover and resolve the intrinsic dependencies of **all** VCS dependencies, whether they are editable or not, to prevent resolution conflicts. pypa#3368
-   Added a new environment variable, `PIPENV_RESOLVE_VCS`, to toggle dependency resolution off for non-editable VCS, file, and URL based dependencies. pypa#3577
-   Added the ability for Windows users to enable emojis by setting `PIPENV_HIDE_EMOJIS=0`. pypa#3595
-   Allow overriding `PIPENV_INSTALL_TIMEOUT` environment variable (in seconds). pypa#3652
-   Allow overriding `PIP_EXISTS_ACTION` evironment variable (value is passed to pip install). Possible values here: <> Useful when you need to `PIP\_EXISTS\_ACTION=i` (ignore existing packages) - great for CI environments, where you need really fast setup. pypa#3738
-   Pipenv will no longer forcibly override `PIP_NO_DEPS` on all vcs and file dependencies as resolution happens on these in a pre-lock step. pypa#3763
-   Improved verbose logging output during `pipenv lock` will now stream output to the console while maintaining a spinner. pypa#3810
-   Added support for automatic python installs via `asdf` and associated `PIPENV_DONT_USE_ASDF` environment variable. pypa#4018
-   Pyenv/asdf can now be used whether or not they are available on PATH. Setting `PYENV_ROOT`/`ASDF_DIR` in a `.env` file allows Pipenv to install an interpreter without any shell customizations, so long as pyenv/asdf is installed. pypa#4245
-   Added `--key` command line parameter for including personal API tokens when running `pipenv check`. pypa#4257

Behavior Changes

-   Make conservative checks of known exceptions when subprocess returns output, so user won\'t see the whole traceback - just the error. pypa#2553
-   Do not touch Pipfile early and rely on it so that one can do `pipenv sync` without a Pipfile. pypa#3386
-   Re-enable `--help` option for `pipenv run` command. pypa#3844
-   Make sure `pipenv lock -r --pypi-mirror {MIRROR_URL}` will respect the pypi-mirror in requirements output. pypa#4199

Bug Fixes

-   Raise `PipenvUsageError` when \[\[source\]\] does not contain url field. pypa#2373
-   Fixed a bug which caused editable package resolution to sometimes fail with an unhelpful setuptools-related error message. pypa#2722
-   Fixed an issue which caused errors due to reliance on the system utilities `which` and `where` which may not always exist on some
-   Fixed a bug which caused periodic failures in python discovery when executables named `python` were not present on the target `$PATH`. pypa#2783
-   Dependency resolution now writes hashes for local and remote files to the lockfile. pypa#3053
-   Fixed a bug which prevented `pipenv graph` from correctly showing all dependencies when running from within `pipenv shell`. pypa#3071
-   Fixed resolution of direct-url dependencies in `` files to respect `PEP-508` style URL dependencies. pypa#3148
-   Fixed a bug which caused failures in warning reporting when running pipenv inside a virtualenv under some circumstances.
-   Fixed a bug with package discovery when running `pipenv clean`. pypa#3298
-   Quote command arguments with carets (`^`) on Windows to work around unintended shell escapes. pypa#3307
-   Handle alternate names for UTF-8 encoding. pypa#3313
-   Abort pipenv before adding the non-exist package to Pipfile. pypa#3318
-   Don\'t normalize the package name user passes in. pypa#3324
-   Fix a bug where custom virtualenv can not be activated with pipenv shell pypa#3339
-   Fix a bug that `--site-packages` flag is not recognized. pypa#3351
-   Fix a bug where `pipenv --clear` is not working pypa#3353
-   Fix unhashable type error during `$ pipenv install --selective-upgrade` pypa#3384
-   Dependencies with direct `PEP508` compliant VCS URLs specified in their `install_requires` will now be successfully locked during the resolution process. pypa#3396
-   Fixed a keyerror which could occur when locking VCS dependencies in
    some cases. pypa#3404
-   Fixed a bug that `ValidationError` is thrown when some fields are missing in source section. pypa#3427
-   Updated the index names in lock file when source name in Pipfile is changed. pypa#3449
-   Fixed an issue which caused `pipenv install --help` to show duplicate entries for `--pre`. pypa#3479
-   Fix bug causing `[SSL: CERTIFICATE_VERIFY_FAILED]` when Pipfile `[[source]]` has `verify_ssl=false` and url with custom port. pypa#3502
-   Fix `sync --sequential` ignoring `pip install` errors and logs. pypa#3537
-   Fix the issue that lock file can\'t be created when `PIPENV_PIPFILE` is not under working directory. pypa#3584
-   Pipenv will no longer inadvertently set `editable=True` on all vcs dependencies. pypa#3647
-   The `--keep-outdated` argument to `pipenv install` and `pipenv lock` will now drop specifier constraints when encountering editable dependencies.
    -   In addition, `--keep-outdated` will retain specifiers that would otherwise be dropped from any entries that have not been updated. pypa#3656
-   Fixed a bug which sometimes caused pipenv to fail to respect the `--site-packages` flag when passed with `pipenv install`. pypa#3718
-   Normalize the package names to lowercase when comparing used and in-Pipfile packages. pypa#3745
-   `pipenv update --outdated` will now correctly handle comparisons between pre/post-releases and normal releases. pypa#3766
-   Fixed a `KeyError` which could occur when pinning outdated VCS dependencies via `pipenv lock --keep-outdated`. pypa#3768
-   Resolved an issue which caused resolution to fail when encountering poorly formatted `python_version` markers in `` and `setup.cfg` files. pypa#3786
-   Fix a bug that installation errors are displayed as a list. pypa#3794
-   Update `pythonfinder` to fix a problem that `python.exe` will be mistakenly chosen for virtualenv creation under WSL. pypa#3807
-   Fixed several bugs which could prevent editable VCS dependencies from being installed into target environments, even when reporting
    successful installation. pypa#3809
-   `pipenv check --system` should find the correct Python interpreter when `python` does not exist on the system. pypa#3819
-   Resolve the symlinks when the path is absolute. pypa#3842
-   Pass `--pre` and `--clear` options to `pipenv update --outdated`. pypa#3879
-   Fixed a bug which prevented resolution of direct URL dependencies which have PEP508 style direct url VCS sub-dependencies with
    subdirectories. pypa#3976
-   Honor `PIPENV_SPINNER` environment variable pypa#4045
-   Fixed an issue with `pipenv check` failing due to an invalid API key from ``. pypa#4188
-   Fixed a bug which caused versions from VCS dependencies to be included in `Pipfile.lock` inadvertently. pypa#4217
-   Fixed a bug which caused pipenv to search non-existent virtual environments for `pip` when installing using `--system`. pypa#4220
-   `Requires-Python` values specifying constraint versions of python starting from `1.x` will now be parsed successfully. pypa#4226
-   Fix a bug of `pipenv update --outdated` that can\'t print output correctly. pypa#4229
-   Fixed a bug which caused pipenv to prefer source distributions over wheels from `PyPI` during the dependency resolution phase. Fixed an issue which prevented proper build isolation using `pep517` based builders during dependency resolution. pypa#4231
-   Don\'t fallback to system Python when no matching Python version is found. pypa#4232

Vendored Libraries

- Updated `pip_shims` to support `--outdated` with new pip versions. pypa#3766
- Update vendored dependencies and invocations
  - Update vendored and patched dependencies
  - Update patches on `piptools`, `pip`, `pip-shims`, `tomlkit`
  - Fix invocations of dependencies
  - Fix custom `InstallCommand` instantiation
  - Update `PackageFinder` usage
  - Fix `Bool` stringify attempts from `tomlkit`
  - Updated vendored dependencies:
    -   **attrs**: `18.2.0 => `19.1.0`
    -   **certifi**: `2018.10.15 => `2019.3.9`
    -   **cached\_property**: `1.4.3 => `1.5.1`
    -   **cerberus**: `1.2.0 => `1.3.1`
    -   **click**: `7.0.0 => `7.1.1`
    -   **click-completion**: `0.5.0 => `0.5.1`
    -   **colorama**: `0.3.9 => `0.4.3`
    -   **contextlib2**: `(new) => `0.6.0.post1`
    -   **distlib**: `0.2.8 => `0.2.9`
    -   **funcsigs**: `(new) => `1.0.2`
    -   **importlib\_metadata** `1.3.0 => `1.5.1`
    -   **importlib-resources**: `(new) => `1.4.0`
    -   **idna**: `2.7 => `2.9`
    -   **jinja2**: `2.10.0 => `2.11.1`
    -   **markupsafe**: `1.0 => `1.1.1`
    -   **more-itertools**: `(new) => `5.0.0`
    -   **orderedmultidict**: `(new) => `1.0`
    -   **packaging**: `18.0 => `19.0`
    -   **parse**: `1.9.0 => `1.15.0`
    -   **pathlib2**: `2.3.2 => `2.3.3`
    -   **pep517**: `(new) => `0.5.0`
    -   **pexpect**: `4.6.0 => `4.8.0`
    -   **pip-shims**: `0.2.0 => `0.5.1`
    -   **pipdeptree**: `0.13.0 => `0.13.2`
    -   **pyparsing**: `2.2.2 => `2.4.6`
    -   **python-dotenv**: `0.9.1 => `0.10.2`
    -   **pythonfinder**: `1.1.10 => `1.2.2`
    -   **pytoml**: `(new) => `0.1.20`
    -   **requests**: `2.20.1 => `2.23.0`
    -   **requirementslib**: `1.3.3 => `1.5.4`
    -   **scandir**: `1.9.0 => `1.10.0`
    -   **shellingham**: `1.2.7 => `1.3.2`
    -   **six**: `1.11.0 => `1.14.0`
    -   **tomlkit**: `0.5.2 => `0.5.11`
    -   **urllib3**: `1.24 => `1.25.8`
    -   **vistir**: `0.3.0 => `0.5.0`
    -   **yaspin**: `0.14.0 => `0.14.3`
    -   **zipp**: `0.6.0`
    - Removed vendored dependency **cursor**. pypa#4169

-   Add and update vendored dependencies to accommodate `safety` vendoring:
    -   **safety** `(none)` => `1.8.7`
    -   **dparse** `(none)` => `0.5.0`
    -   **pyyaml** `(none)` => `5.3.1`
    -   **urllib3** `1.25.8` => `1.25.9`
    -   **certifi** `2019.11.28` => `2020.4.5.1`
    -   **pyparsing** `2.4.6` => `2.4.7`
    -   **resolvelib** `0.2.2` => `0.3.0`
    -   **importlib-metadata** `1.5.1` => `1.6.0`
    -   **pip-shims** `0.5.1` => `0.5.2`
    -   **requirementslib** `1.5.5` => `1.5.6` pypa#4188

-   Updated vendored `pip` => `20.0.2` and `pip-tools` => `5.0.0`. pypa#4215
-   Updated vendored dependencies to latest versions for security and bug fixes:
    -   **requirementslib** `1.5.8` => `1.5.9`
    -   **vistir** `0.5.0` => `0.5.1`
    -   **jinja2** `2.11.1` => `2.11.2`
    -   **click** `7.1.1` => `7.1.2`
    -   **dateutil** `(none)` => `2.8.1`
    -   **backports.functools\_lru\_cache** `1.5.0` => `1.6.1`
    -   **enum34** `1.1.6` => `1.1.10`
    -   **toml** `0.10.0` => `0.10.1`
    -   **importlib\_resources** `1.4.0` => `1.5.0` pypa#4226
-   Changed attrs import path in vendored dependencies to always import from `pipenv.vendor`. pypa#4267

Improved Documentation

-   Added documenation about variable expansion in `Pipfile` entries. pypa#2317
-   Consolidate all contributing docs in the rst file pypa#3120
-   Update the out-dated manual page. pypa#3246
-   Move CLI docs to its own page. pypa#3346
-   Replace (non-existant) video on docs index.rst with equivalent gif. pypa#3499
-   Clarify wording in Basic Usage example on using double quotes to escape shell redirection pypa#3522
-   Ensure docs show navigation on small-screen devices pypa#3527
-   Added a link to the TOML Spec under General Recommendations & Version Control to clarify how Pipfiles should be written. pypa#3629
-   Updated the documentation with the new `pytest` entrypoint. pypa#3759
-   Fix link to GIF in demonstrating Pipenv\'s usage, and add descriptive alt text. pypa#3911
-   Added a line describing potential issues in fancy extension. pypa#3912
-   Documental description of how Pipfile works and association with Pipenv. pypa#3913
-   Clarify the proper value of `python_version` and `python_full_version`. pypa#3914
-   Write description for `--deploy` extension and few extensions differences. pypa#3915
-   More documentation for `.env` files pypa#4100
-   Updated documentation to point to working links. pypa#4137
-   Replace with pypa#4167
-   Added functionality to check spelling in documentation and cleaned up existing typographical issues. pypa#4209
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Priority: Medium Status: Needs More Information Type: Discussion Type: Possible Bug
None yet

Successfully merging a pull request may close this issue.

6 participants