[Solved] `cl-update` is broken

Discussions & Opinions
1

Hi folks,
for many months I cannot use cl-update (I use regular Gentoo emerge to maintain my system).
The issue seems to be missing package:

# cl-update
Traceback (most recent call last):
  File "/usr/lib/python3.13/site-packages/calculate/core/core_main.py", line 46, in core_main
    sys.exit(main())
             ~~~~^^
  File "/usr/lib/python3.13/site-packages/calculate/core/server/func.py", line 1972, in wrapper
    return func(*args, **kwargs)
  File "/usr/lib/python3.13/site-packages/calculate/core/server/cl_server.py", line 232, in main
    outer_wsdl_classes = initialization(cl_wsdl)
  File "/usr/lib/python3.13/site-packages/calculate/core/server/func.py", line 1700, in initialization
    cl_wsdl_core = importlib.import_module(module_name)
  File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
  File "/usr/lib/python3.13/site-packages/calculate/install/wsdl_install.py", line 22, in <module>
    from . import install
  File "/usr/lib/python3.13/site-packages/calculate/install/install.py", line 59, in <module>
    from .migrate_users import migrate
  File "/usr/lib/python3.13/site-packages/calculate/install/migrate_users.py", line 18, in <module>
    from calculate.lib.encrypt import encrypt
  File "/usr/lib/python3.13/site-packages/calculate/lib/encrypt.py", line 21, in <module>
    import crypt
ModuleNotFoundError: No module named 'crypt'
No module named 'crypt'

However, when I install it:

$ pip install crypto
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: crypto in ./.local/lib/python3.13/site-packages (1.4.1)
Requirement already satisfied: Naked in ./.local/lib/python3.13/site-packages (from crypto) (0.1.32)
Requirement already satisfied: shellescape in ./.local/lib/python3.13/site-packages (from crypto) (3.8.1)
Requirement already satisfied: requests in /usr/lib/python3.13/site-packages (from Naked->crypto) (2.32.4)
Requirement already satisfied: pyyaml in /usr/lib/python3.13/site-packages (from Naked->crypto) (6.0.2)
Requirement already satisfied: charset_normalizer<4,>=2 in /usr/lib/python3.13/site-packages (from requests->Naked->crypto) (3.4.2)
Requirement already satisfied: idna<4,>=2.5 in /usr/lib/python3.13/site-packages (from requests->Naked->crypto) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/lib/python3.13/site-packages (from requests->Naked->crypto) (2.5.0)
Requirement already satisfied: certifi>=2017.4.17 in /usr/lib/python3.13/site-packages (from requests->Naked->crypto) (3024.7.22)

And run the cl-update again, it will “spin the text wheel” and hang forever:

$ cl-update
/No module named 'crypt'
|

Any ideas?

2

What will return:

$ equery list -op calculate-utils

 * Searching for calculate-utils ...
[--O] [  ] sys-apps/calculate-utils-3.7.7.11:0
[--O] [ ~] sys-apps/calculate-utils-3.7.7.12:0
[--O] [ ~] sys-apps/calculate-utils-3.7.7.13:0
[--O] [  ] sys-apps/calculate-utils-3.7.7.14:0
[--O] [ ~] sys-apps/calculate-utils-3.7.8:0
[--O] [  ] sys-apps/calculate-utils-3.7.8.1:0
[--O] [  ] sys-apps/calculate-utils-3.7.8.2:0
[I-O] [  ] sys-apps/calculate-utils-3.7.8.3:0
[--O] [ -] sys-apps/calculate-utils-9999:0

Try reinstalling this package, maybe it will pull in the dependencies?

$ equery files calculate-utils | grep -i encrypt[.]py

/usr/lib/python3.12/site-packages/calculate/lib/encrypt.py

$ equery belongs /usr/lib/python3.12/site-packages/calculate/lib/encrypt.py

 * Searching for /usr/lib/python3.12/site-packages/calculate/lib/encrypt.py ...
sys-apps/calculate-utils-3.7.8.3 (/usr/lib/python3.12/site-packages/calculate/lib/encrypt.py)

$ whereis cl-update

cl-update: /usr/bin/cl-update

$ equery belongs /usr/bin/cl-update

 * Searching for /usr/bin/cl-update ...
sys-apps/calculate-utils-3.7.8.3 (/usr/bin/cl-update -> ../libexec/calculate/cl-core-wrapper)
sys-apps/calculate-utils-3.7.8.3 (/usr/libexec/calculate/cl-core-wrapper)
3

Спасибо, NickM

$ equery list -op calculate-utils
 * Searching for calculate-utils ...
[--O] [  ] sys-apps/calculate-utils-3.7.7.11:0
[--O] [ ~] sys-apps/calculate-utils-3.7.7.12:0
[--O] [ ~] sys-apps/calculate-utils-3.7.7.13:0
[--O] [  ] sys-apps/calculate-utils-3.7.7.14:0
[--O] [ ~] sys-apps/calculate-utils-3.7.8:0
[--O] [  ] sys-apps/calculate-utils-3.7.8.1:0
[--O] [  ] sys-apps/calculate-utils-3.7.8.2:0
[I-O] [  ] sys-apps/calculate-utils-3.7.8.3:0
[--O] [ -] sys-apps/calculate-utils-9999:0

$ equery belongs /usr/lib/python3.13/site-packages/calculate/lib/encrypt.py
 * Searching for /usr/lib/python3.13/site-packages/calculate/lib/encrypt.py ... 
sys-apps/calculate-utils-3.7.8.3 (/usr/lib/python3.13/site-packages/calculate/lib/encrypt.py)

I already reinstalled this package and everything, and cl-update still fail.
But, I’ve noticed emerge complains about non-existing set autodeps. Once I removed it the dependencies has been re-calculated and now some 250 packages are being emerge. Hope that helps! Will post a result here soon.

4

Why do you have this package with dependencies to “python 3.13”, when, “by default”, “python 3.12” is specified in the flags?

$ equery uses calculate-utils

[ Legend : U - final flag setting for installation]
[        : I - package is installed with flag     ]
[ Colors : set, unset                             ]
 * Found these USE flags for sys-apps/calculate-utils-3.7.8.3:
 U I
 + + backup                    : Include backup module
 + + client                    : Include module for setting and storing the user accounts in the domain
 + + console                   : Include console module
 + + dbus                      : Enable ability to run core server by DBus
 - - debug                     : Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces
 + + desktop                   : Include module for desktop configuration
 + + gpg                       : Enable the signature checking
 + + install                   : Enable support for disk installation
 - - minimal                   : Use minimal depends for Calculate install
 - - pxe                       : Enable support for PXE installation
 - - python_targets_python3_11 : Build with Python 3.11
 + + python_targets_python3_12 : Build with Python 3.12
 - - python_targets_python3_13 : Build with Python 3.13
 + + qt6                       : Include Qt 6 GUI console

$ eix calculate-utils

[I] sys-apps/calculate-utils [1]
     Доступные версии:      3.7.7.11 ~3.7.7.12 ~3.7.7.13 3.7.7.14 ~3.7.8 3.7.8.1 3.7.8.2 3.7.8.3 **9999*l {backup client console dbus debug desktop +gpg +install minimal pxe qt6 PYTHON_TARGETS="python3_11 python3_12 python3_13"}
     Установленные версии:  3.7.8.3(16:20:35 17.07.2025)(backup client console dbus desktop gpg install qt6 -debug -minimal -pxe PYTHON_TARGETS="python3_12 -python3_11 -python3_13")
     Домашняя страница:     https://www.calculate-linux.org/main/en/calculate_utilities
     Описание:              A set of Calculate utilities for system installation, build and upgrade

[1] "calculate" /var/db/repos/calculate
5

I did not set any direct dependencies to python-3.13, I only extended the PYTHON_TARGETS in the /etc/portage/make.conf/custom

I am using the same version string as you (=sys-apps/calculate-utils-3.7.8.3)

$ eix calculate-utils
[I] sys-apps/calculate-utils [1]
     Available versions:  3.7.7.11 ~3.7.7.12 ~3.7.7.13 3.7.7.14 ~3.7.8 3.7.8.1 3.7.8.2 3.7.8.3 **9999*l {backup client console dbus debug desktop +gpg +install minimal pxe qt6 PYTHON_TARGETS="python3_11 python3_12 python3_13"}
     Installed versions:  3.7.8.3(11:15:21 PM 07/18/2025)(backup client console dbus desktop gpg install qt6 -debug -minimal -pxe PYTHON_TARGETS="python3_11 python3_12 python3_13")
     Homepage:            https://www.calculate-linux.org/main/en/calculate_utilities
     Description:         A set of Calculate utilities for system installation, build and upgrade

[1] "calculate" /var/db/repos/calculate

This is what calculate-utils uses:

[ Legend : U - final flag setting for installation]
[        : I - package is installed with flag     ]
[ Colors : set, unset                             ]
 * Found these USE flags for sys-apps/calculate-utils-3.7.8.3:
 U I
 + + backup                    : Include backup module
 + + client                    : Include module for setting and storing the user accounts in the domain
 + + console                   : Include console module
 + + dbus                      : Enable ability to run core server by DBus
 - - debug                     : Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see
                                 https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces
 + + desktop                   : Include module for desktop configuration
 + + gpg                       : Enable the signature checking
 + + install                   : Enable support for disk installation
 - - minimal                   : Use minimal depends for Calculate install
 - - pxe                       : Enable support for PXE installation
 + + python_targets_python3_11 : Build with Python 3.11
 + + python_targets_python3_12 : Build with Python 3.12
 + + python_targets_python3_13 : Build with Python 3.13
 + + qt6                       : Include Qt 6 GUI console

As you can see all python3 version flags are there.

6

Now it is clear why calculate-utils requires you to have “python 3.13”, which lacks the modules specified in the error of the first message.

7

Food for thought:

crypt — Function to check Unix passwords — Python 3.13.5 documentation

8

Shouldn’t the required packages be fetched for every python version used in the system?

9

Ok, now it makes sense why it is not working in python3.13.
Will remove 3.13 from make.conf and re-emerge the world.

FYI. Amongst the issues I’m solving, the cl-update is just the first in a row. I’ll post a separate thread for them.

10

What’s the result? Are your questions resolved?

11

@NickM yes, removing python3_13 from the make.conf/ and emerging the word set did bring cl-update back to life. Thanks for your help!