Yay -S anki, conflicting files

Trying to install anki from aur results in error pointing to “six”

I “sudo pacman -S qt6-multimedia-ffmpeg” before “yay -S anki” and the result is the same minus the warning.

yay -S anki                                                                   ✔  47s  
:: There are 2 providers available for cargo:
:: Repository extra
    1) rust 
:: Repository community
    2) rustup 

Enter a number (default=1): 
==> 2
AUR Explicit (1): anki-2.1.61-1
Sync Dependency (11): python-waitress-2.1.2-1, python-orjson-3.8.9-1, python-pyqt6-webengine-6.4.0-1, qt6-multimedia-6.4.3-1, python-protobuf-21.12-1, python-pysocks-1.7.1-7, python-flask-cors-3.0.10-4, python-beautifulsoup4-4.11.2-1, python-decorator-5.1.1-2, python-send2trash-1.8.0-3, python-markdown-3.4.3-1
Sync Make Dependency (5): ninja-1.11.1-2, nodejs-19.8.1-1, rustup-1.25.2-1, libxcrypt-compat-4.4.33-1, python-installer-0.7.0-1
:: PKGBUILD up to date, skipping download: anki
  1 anki                                     (Build Files Exist)
==> Packages to cleanBuild?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> N
  1 anki                                     (Build Files Exist)
==> Diffs to show?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> N
==> Making package: anki 2.1.61-1 (tor 20 apr 2023 15:54:38)
==> Retrieving sources...
  -> Updating anki git repo...
  -> Found no-update.patch
==> Validating source files with sha256sums...
    anki ... Skipped
    no-update.patch ... Passed
==> Verifying source file signatures with gpg...
    anki git repo ... Passed
:: Remove make dependencies after install? [y/N] y
:: (1/1) Parsing SRCINFO: anki
pub   rsa4096 2018-09-16 [C]
uid           [ unknown] Anki Signatures <gpg@ankiweb.net>
sub   rsa4096 2018-09-16 [S]

resolving dependencies...
:: There are 2 providers available for qt6-multimedia-backend:
:: Repository extra
   1) qt6-multimedia-ffmpeg  2) qt6-multimedia-gstreamer

Enter a number (default=1): 1
looking for conflicting packages...
warning: dependency cycle detected:
warning: qt6-multimedia-ffmpeg will be installed before its qt6-multimedia dependency

Packages (28) python-click-8.1.3-1  python-flask-2.2.2-1  python-itsdangerous-2.1.2-2  python-pyqt6-6.4.2-1
              python-pyqt6-sip-13.4.1-1  python-six-1.16.0-6  python-soupsieve-2.4-1  python-werkzeug-2.2.3-1
              qt6-multimedia-ffmpeg-6.4.3-1  qt6-positioning-6.4.3-1  qt6-webchannel-6.4.3-1  qt6-webengine-6.4.3-1
              libxcrypt-compat-4.4.33-1  ninja-1.11.1-2  nodejs-19.8.1-1  python-beautifulsoup4-4.11.2-1  python-decorator-5.1.1-2
              python-flask-cors-3.0.10-4  python-installer-0.7.0-1  python-markdown-3.4.3-1  python-orjson-3.8.9-1
              python-protobuf-21.12-1  python-pyqt6-webengine-6.4.0-1  python-pysocks-1.7.1-7  python-send2trash-1.8.0-3
              python-waitress-2.1.2-1  qt6-multimedia-6.4.3-1  rustup-1.25.2-1

Total Installed Size:  300,29 MiB

:: Proceed with installation? [Y/n] y
(28/28) checking keys in keyring                                                [##############################################] 100%
(28/28) checking package integrity                                              [##############################################] 100%
(28/28) loading package files                                                   [##############################################] 100%
(28/28) checking for file conflicts                                             [##############################################] 100%
error: failed to commit transaction (conflicting files)
python-six: /usr/lib/python3.10/site-packages/__pycache__/six.cpython-310.pyc exists in filesystem
python-six: /usr/lib/python3.10/site-packages/six.py exists in filesystem
Errors occurred, no packages were upgraded.
error: could not set install reason for package python-waitress (could not find or read package)
error: could not set install reason for package python-pysocks (could not find or read package)
error: could not set install reason for package rustup (could not find or read package)
error: could not set install reason for package python-flask-cors (could not find or read package)
error: could not set install reason for package libxcrypt-compat (could not find or read package)
error: could not set install reason for package python-decorator (could not find or read package)
error: could not set install reason for package python-installer (could not find or read package)
error: could not set install reason for package python-pyqt6-webengine (could not find or read package)
error: could not set install reason for package ninja (could not find or read package)
error: could not set install reason for package nodejs (could not find or read package)
error: could not set install reason for package python-send2trash (could not find or read package)
error: could not set install reason for package python-orjson (could not find or read package)
error: could not set install reason for package qt6-multimedia (could not find or read package)
error: could not set install reason for package python-protobuf (could not find or read package)
error: could not set install reason for package python-beautifulsoup4 (could not find or read package)
error: could not set install reason for package python-markdown (could not find or read package)
 -> Failed to install layer, rolling up to next layer.error:error installing repo packages

looking in to what six is and if it is a dependency in the pip package system

Name: six
Version: 1.16.0
Summary: Python 2 and 3 compatibility utilities
Home-page: https://github.com/benjaminp/six
Author: Benjamin Peterson
Author-email: benjamin@python.org
License: MIT
Location: /usr/lib/python3.10/site-packages

looking into if it is a dependency in the pacman package system

pacman -Qo /usr/lib/python3.10/site-packages/six.py
error: No package owns /usr/lib/python3.10/site-packages/six.py

since it seems to be an orphan, trying to remove it.

pip uninstall six                                                      INT ✘  2m 36s  
Found existing installation: six 1.16.0
Uninstalling six-1.16.0:
  Would remove:
Proceed (Y/n)? y
ERROR: Exception:
Traceback (most recent call last):
  File "/usr/lib/python3.10/shutil.py", line 816, in move
    os.rename(src, real_dst)
OSError: [Errno 18] Invalid cross-device link: '/usr/lib/python3.10/site-packages/__pycache__/six.cpython-310.pyc' -> '/tmp/pip-uninstall-zo2uj77w/six.cpython-310.pyc'

and so on...

What is wrong and how can I fix it?

Don’t use sudo with pip.

So how do I fix it?

If I have sudo pip installed packages, how can I find them?
Will ‘sudo pip uninstall package-name’ not remove all of what ‘sudo pip install package-name’ installed?
I have not activated any log.

all of the packages are owner root and I think most of the packages are from pacman or yay.

I have googled a lot but I have not found a solution on how to find the sudo installed package that I can uninstall to make the problem go away.

A question about moving forward. pipx and pip venv:
It seems like pipx creates an environment for each package, hence a lot of duplication in files. Also a package will not be able to use an other package as a dependency.
pip venv: you can create a virtual environment where all the packages can use each other as dependencies but the installed packages from yay and pacman will not be able to use the packages installed in the virtual environment as dependencies.
So if I install a python package (dependency) to support an installation with pacman I have to install it with ‘pip install’. I.e. install gns3-webclient-pack . The guide they say I should use ‘sudo pip install’. This is a support installation of the application GNS3. Is there anything about the communication between the installation of GNS3 and the webclient-pack that will break if I do not use sudo? I was thinking perhaps they have hardcoded the path to the application, then it will break if I do not use sudo?

Is this correct, do you know?

Never sync new packages using -S only - unless you know your system is 100% up-to-data

To have pip installed on your system - no need to suffix with version as only one python exist - Python 3.x

sudo pacman -Syu python-pip

Exploit the --user argument to pip install e.g.

 $ python -m pip install --user gns3-webclient-pack
Collecting gns3-webclient-pack
  Downloading gns3-webclient-pack-1.0.0b4.tar.gz (173 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 173.2/173.2 kB 7.1 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: distro==1.8.0 in /usr/lib/python3.10/site-packages (from gns3-webclient-pack) (1.8.0)
Building wheels for collected packages: gns3-webclient-pack
  Building wheel for gns3-webclient-pack (setup.py) ... done
  Created wheel for gns3-webclient-pack: filename=gns3_webclient_pack-1.0.0b4-py3-none-any.whl size=168147 sha256=51e9a4f620936b663efe4b5967e38c2c3336e9648330fec8cee23df494491b3a
  Stored in directory: /home/fh/.cache/pip/wheels/12/9e/f2/5db9ca3b35832985c8b24d7aabcb3612dbbc78e457f0e7df90
Successfully built gns3-webclient-pack
Installing collected packages: gns3-webclient-pack
Successfully installed gns3-webclient-pack-1.0.0b4

Also check what is available using AUR - as those will be installed using the package manager and thus tracked and conflicts are avoided.

A second note is on GNS3 - as the general recommandation is use a virtual machine - and not your workstation.

The webclient README also contains instruction to use sudo npm -g - this is also a source of problem when using Manjaro.

In fact a lot of things works differently on Manjaro (actually on any Arch based distribution).

This is primarily due to the K.I.S.S principle (there can be only one version of any given library) and as such you should carefully convert Ubuntu or Fedora instructions to Manjaro equivalents - taking into account how pacman with libalpm handles the system dependencies.

For the same of clarification I have executed an installation of anki with no issues.

 $ pamac build anki
Checking anki dependencies...
Choose a provider for qt6-multimedia-backend:
1:  qt6-multimedia-ffmpeg     6.5.0-1  extra
2:  qt6-multimedia-gstreamer  6.5.0-1  extra

Enter a number (default=1): 1

Choose a provider for cargo:
1:  rust    1:1.69.0-3  extra
2:  rustup  1.26.0-1    community

Enter a number (default=1): 1

Resolving dependencies...
Checking inter-conflicts...
Warning: dependency cycle detected:
Warning: qt6-multimedia will be installed before its qt6-multimedia-ffmpeg dependency

To install (30):
  python-werkzeug         2.2.3-1     (Required By: anki)  community  347,0 kB
  python-itsdangerous     2.1.2-2     (Required By: anki)  community  25,5 kB
  python-click            8.1.3-1     (Required By: anki)  community  158,5 kB
  python-flask            2.2.2-1     (Required By: anki)  community  144,7 kB
  python-six              1.16.0-6    (Required By: anki)  extra      23,8 kB
  python-flask-cors       3.0.10-4    (Required By: anki)  community  20,4 kB
  python-send2trash       1.8.0-3     (Required By: anki)  community  25,9 kB
  python-pyqt6-sip        13.5.1-1    (Required By: anki)  extra      70,2 kB
  ninja                   1.11.1-2    (Required By: anki)  community  148,9 kB
  python-installer        0.7.0-1     (Required By: anki)  community  117,5 kB
  python-protobuf         21.12-1     (Required By: anki)  extra      305,6 kB
  libxcrypt-compat        4.4.33-1    (Required By: anki)  core       69,8 kB
  qt6-positioning         6.5.0-1     (Required By: anki)  extra      374,2 kB
  python-pysocks          1.7.1-7     (Required By: anki)  community  27,7 kB
  python-attrs            22.2.0-1    (Required By: anki)  extra      87,2 kB
  python-pyrsistent       0.19.3-1    (Required By: anki)  community  98,3 kB
  python-jsonschema       4.17.3-1    (Required By: anki)  community  140,1 kB
  python-waitress         2.1.2-1     (Required By: anki)  community  84,3 kB
  python-pyqt6            6.5.0-1     (Required By: anki)  extra      4,3 MB
  python-markdown         3.4.3-1     (Required By: anki)  community  129,9 kB
  python-soupsieve        2.4-1       (Required By: anki)  community  66,2 kB
  qt6-webchannel          6.5.0-1     (Required By: anki)  extra      121,4 kB
  qt6-webengine           6.5.0-2     (Required By: anki)  extra      71,3 MB
  qt6-multimedia          6.5.0-1     (Required By: anki)  extra      945,0 kB
  qt6-multimedia-ffmpeg   6.5.0-1     (Required By: anki)  extra      136,7 kB
  python-beautifulsoup4   4.11.2-1    (Required By: anki)  community  207,6 kB
  python-orjson           3.8.10-1    (Required By: anki)  community  249,5 kB
  rust                    1:1.69.0-2  (Required By: anki)  extra      86,6 MB
  python-decorator        5.1.1-2     (Required By: anki)  community  16,6 kB
  python-pyqt6-webengine  6.5.0-1     (Required By: anki)  extra      122,8 kB
To build (1):
  anki                    2.1.61-1                         AUR

Total download size: 166,4 MB
Total installed size: 721,4 MB

Edit build files : [e] 
Apply transaction ? [e/y/N] y

Cloning anki build files...
Generating anki information...
The PGP key 814EA4E90C34AF39A712DE703F5566A2D16899FB is needed to verify anki source files.
Trust Anki Signatures <gpg@ankiweb.net> and import the PGP key ? [y/N] y
gpg: key 0x3F5566A2D16899FB: public key "Anki Signatures <gpg@ankiweb.net>" imported
gpg: Total number processed: 1
gpg:               imported: 1

==== AUTHENTICATING FOR org.manjaro.pamac.commit ====
Authentication is required to install, update, or remove packages
Authenticating as: fh
Download of python-werkzeug (2.2.3-1) started                                                                 
Download of python-itsdangerous (2.1.2-2) started                                                             
Download of python-itsdangerous (2.1.2-2) finished                                                            
Download of python-flask (2.2.2-1) started                                                                    
Download of python-werkzeug (2.2.3-1) finished                                                                
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Download of python-click (8.1.3-1) started                                                                    
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Download of python-flask-cors (3.0.10-4) started                                                              
Download of python-flask-cors (3.0.10-4) finished                                                             
Download of ninja (1.11.1-2) started                                                                          
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Download of python-beautifulsoup4 (4.11.2-1) started                                                          
Download of python-beautifulsoup4 (4.11.2-1) finished                                                         
Download of qt6-webchannel (6.5.0-1) started                                                                  
Download of qt6-webchannel (6.5.0-1) finished                                                                 
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Download of qt6-webengine (6.5.0-2) started                                                                   
Download of python-pyrsistent (0.19.3-1) started                                                              
Download of python-pyrsistent (0.19.3-1) finished                                                             
Download of qt6-positioning (6.5.0-1) started                                                                 
Download of qt6-positioning (6.5.0-1) finished                                                                
Download of python-pysocks (1.7.1-7) started                                                                  
Download of python-pysocks (1.7.1-7) finished                                                                 
Download of python-jsonschema (4.17.3-1) started                                                              
Download of python-jsonschema (4.17.3-1) finished                                                             
Download of python-pyqt6 (6.5.0-1) started                                                                    
Download of python-pyqt6 (6.5.0-1) finished                                                                   
Download of python-waitress (2.1.2-1) started                                                                 
Download of python-waitress (2.1.2-1) finished                                                                
Download of rust (1:1.69.0-3) started                                                                         
Download of qt6-webengine (6.5.0-2) finished                                                                  
Download of python-decorator (5.1.1-2) started                                                                
Download of python-decorator (5.1.1-2) finished                                                               
Download of python-markdown (3.4.3-1) started                                                                 
Download of python-markdown (3.4.3-1) finished                                                                
Download of qt6-multimedia-ffmpeg (6.5.0-1) started                                                           
Download of qt6-multimedia-ffmpeg (6.5.0-1) finished                                                          
Download of qt6-multimedia (6.5.0-1) started                                                                  
Download of qt6-multimedia (6.5.0-1) finished                                                                 
Download of python-pyqt6-webengine (6.5.0-1) started                                                          
Download of python-pyqt6-webengine (6.5.0-1) finished                                                         
Download of python-orjson (3.8.11-1) started                                                                  
Download of python-orjson (3.8.11-1) finished                                                                 
Download of libxcrypt-compat (4.4.33-1) started                                                               
Download of libxcrypt-compat (4.4.33-1) finished                                                              
Download of rust (1:1.69.0-3) finished                                                                        
Checking keyring...                                                                                    [30/30]
Checking integrity...                                                                                  [30/30]
Loading packages files...                                                                              [30/30]
Checking file conflicts...                                                                             [30/30]
Checking available disk space...                                                                       [30/30]
Installing python-werkzeug (2.2.3-1)...                                                                 [1/30]
Installing python-itsdangerous (2.1.2-2)...                                                             [2/30]
Installing python-click (8.1.3-1)...                                                                    [3/30]
Installing python-flask (2.2.2-1)...                                                                    [4/30]
Installing python-six (1.16.0-6)...                                                                     [5/30]
Installing python-flask-cors (3.0.10-4)...                                                              [6/30]
Installing python-send2trash (1.8.0-3)...                                                               [7/30]
Installing python-pyqt6-sip (13.5.1-1)...                                                               [8/30]
Installing ninja (1.11.1-2)...                                                                          [9/30]
Installing python-installer (0.7.0-1)...                                                               [10/30]
Installing python-protobuf (21.12-1)...                                                                [11/30]
Installing python-soupsieve (2.4-1)...                                                                 [12/30]
Installing python-beautifulsoup4 (4.11.2-1)...                                                         [13/30]
Installing qt6-webchannel (6.5.0-1)...                                                                 [14/30]
Installing qt6-positioning (6.5.0-1)...                                                                [15/30]
Installing qt6-webengine (6.5.0-2)...                                                                  [16/30]
Installing python-attrs (22.2.0-1)...                                                                  [17/30]
Installing python-pyrsistent (0.19.3-1)...                                                             [18/30]
Installing python-jsonschema (4.17.3-1)...                                                             [19/30]
Installing python-pysocks (1.7.1-7)...                                                                 [20/30]
Installing python-pyqt6 (6.5.0-1)...                                                                   [21/30]
Installing rust (1:1.69.0-3)...                                                                        [22/30]
Installing python-waitress (2.1.2-1)...                                                                [23/30]
Installing python-decorator (5.1.1-2)...                                                               [24/30]
Installing python-markdown (3.4.3-1)...                                                                [25/30]
Installing qt6-multimedia-ffmpeg (6.5.0-1)...                                                          [26/30]
Installing qt6-multimedia (6.5.0-1)...                                                                 [27/30]
Installing python-pyqt6-webengine (6.5.0-1)...                                                         [28/30]
Installing python-orjson (3.8.11-1)...                                                                 [29/30]
Installing libxcrypt-compat (4.4.33-1)...                                                              [30/30]
Running post-transaction hooks...
Arming ConditionNeedsUpdate...                                                                           [1/2]
Refreshing PackageKit...                                                                                 [2/2]

Building anki...
==> Making package: anki 2.1.61-1 (søn 30 apr 2023 12:08:24 CEST)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Cloning anki git repo...
Cloning into bare repository '/var/tmp/pamac-build-fh/anki/anki'...
remote: Enumerating objects: 148496, done.
remote: Counting objects: 100% (721/721), done.
remote: Compressing objects: 100% (361/361), done.
remote: Total 148496 (delta 388), reused 591 (delta 358), pack-reused 147775
Receiving objects: 100% (148496/148496), 75.26 MiB | 12.13 MiB/s, done.
Resolving deltas: 100% (116651/116651), done.
  -> Found no-update.patch
==> Validating source files with sha256sums...
    anki ... Skipped
    no-update.patch ... Passed
==> Verifying source file signatures with gpg...
    anki git repo ... Passed
==> Removing existing $srcdir/ directory...
==> Extracting sources...
  -> Creating working copy of anki git repo...
Cloning into 'anki'...
Switched to a new branch 'makepkg'
==> Starting prepare()...
patching file qt/aqt/update.py
==> Starting pkgver()...
==> Starting build()...
    Updating git repository `https://github.com/ankitects/rust-csv.git`
    Updating crates.io index
    Updating git repository `https://github.com/ankitects/linkcheck.git`
  Downloaded backtrace v0.3.67
  Downloaded form_urlencoded v1.1.0
  Downloaded cpufeatures v0.2.5
  Downloaded jobserver v0.1.25
  Downloaded h2 v0.3.15
  Downloaded hmac v0.12.1
  Downloaded futures-task v0.3.25
  Downloaded cc v1.0.78
  Downloaded tower-service v0.3.2
  Downloaded constant_time_eq v0.1.5
  Downloaded is-terminal v0.4.2
  Downloaded autocfg v1.1.0
  Downloaded block-buffer v0.10.3
  Downloaded phf_shared v0.11.1
  Downloaded pbkdf2 v0.11.0
  Downloaded zstd-safe v6.0.2+zstd.1.5.2
  Downloaded either v1.8.0
  Downloaded bzip2 v0.4.4
  Downloaded futures-sink v0.3.25
  Downloaded subtle v2.4.1
  Downloaded futures-macro v0.3.25
  Downloaded opaque-debug v0.3.0
  Downloaded sha1 v0.10.5
  Downloaded itoa v1.0.5
  Downloaded prost v0.11.6
  Downloaded once_cell v1.17.0
  Downloaded zstd-safe v5.0.2+zstd.1.5.2
  Downloaded tokio-macros v1.8.2
  Downloaded generic-array v0.14.6
  Downloaded os_str_bytes v6.4.1
  Downloaded futures-core v0.3.25
  Downloaded termcolor v1.2.0
  Downloaded junction v0.2.0
  Downloaded zstd v0.11.2+zstd.1.5.2
  Downloaded tracing-attributes v0.1.23
  Downloaded crypto-common v0.1.6
  Downloaded clap_derive v4.1.0
  Downloaded getrandom v0.1.16
  Downloaded snafu-derive v0.7.4
  Downloaded sha2 v0.10.6
  Downloaded rustc-demangle v0.1.21
  Downloaded password-hash v0.4.2
  Downloaded quote v1.0.23
  Downloaded proc-macro-error-attr v1.0.4
  Downloaded pin-project-lite v0.2.9
  Downloaded zstd v0.12.2+zstd.1.5.2
  Downloaded digest v0.10.6
  Downloaded prost-derive v0.11.6
  Downloaded base64ct v1.5.3
  Downloaded parking_lot_core v0.9.6
  Downloaded crossbeam-utils v0.8.14
  Downloaded time-macros v0.2.6
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     Running `out/rust/debug/configure`
[76/76; 1 active; 103.471s] wheels:anki

Build succeeded.
wheels are in out/wheels
==> Entering fakeroot environment...
==> Starting package()...
==> Tidying install...
  -> Removing libtool files...
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==> Checking for packaging issues...
==> WARNING: Package contains reference to $srcdir
==> Creating package "anki"...
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==> Leaving fakeroot environment.
==> Finished making: anki 2.1.61-1 (søn 30 apr 2023 12:11:31 CEST)
==> Cleaning up...

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Transaction successfully finished.

A fast check in /usr/lib/python3.10/site-packages with
pacman -Qo * | grep error
gives me that:
error: No package owns pyflakes
error: No package owns pyflakes-3.0.1.dist-info
error: No package owns six-1.16.0.dist-info
error: No package owns six.py

I do not think I manually installed any of these packages.
pyflake is a program that checks .py files for errors.
six is a compatibility library.
I do not know how to check what package could have install them or if they are important.
Suggestions on that would be appreciated.

So I uninstalled both of the packages and could install anki.
I do not know why I could not uninstall six before.
Looking back at my first post, perhaps I did not use “sudo pip uninstall” or now I did uninstall pyflakes before I uninstalled six.

On the note about GNS3, why is it prefered to use the vm install?
I could not get the vm working properly. I.e. the terminals could not open in in xfce and importing appliance did not work. Both probably a settings error, I did not spend a lot of time researching it but I could not find information on how to make it work.
Some tutorials for linux uses GNS3 installed locally and what I could read form the GNS3 documentation, it is recommended for non linux users to use the vm but for linux users you get one layer less and performance becomes better on a local install.
Could you elaborate why you think the vm is better?

Also, what is the difference between “pip install --user” and “pip install”. For me pip install ends up under ~/.local …

Thanks for all the help.

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