Install fails - ModuleNotFoundError: No module named 'pymysql'

ingolevin commented 2 years ago

Description

Install of 8.0.5~ynh1 fails with a missing dependency error for module pymysql

2021-11-21 09:15:33,956: DEBUG - Traceback (most recent call last):
2021-11-21 09:15:33,957: DEBUG -   File "setup-seafile-mysql.py", line 19, in <module>
2021-11-21 09:15:33,958: DEBUG -     import pymysql
2021-11-21 09:15:33,959: DEBUG - ModuleNotFoundError: No module named 'pymysql'

Context

Hardware: Raspi4
YunoHost version: 4.3.3
I have access to my server: Through SSH | through the webadmin
Are you in a special context or did you perform some particular tweaking on your YunoHost instance?: no
Using, or trying to install package version/branch: Seafile 8.0.5~ynh1

Logs

https://paste.yunohost.org/raw/qocowazexo

Gilbog commented 2 years ago

I have the same problem! Any leads, anyone?

p1yn5ju6 commented 2 years ago

I have the same problem! Any leads, anyone?

I had the pymysql issue and the numpy issue. But I'm so fed up for having NextCloud working for 5 mins and then breaking itself, that I've been keen to try SF.

I have just managed to install SeaFile on a RPi4 using the official Yuno installer. First though, I logged into my Yuno server, and using the command line performed the usual updates. Then I figured the best thing to do would be to install in advance the modules the installer is complaining about.

I didn't manage to find Numpy but I did get pymysql installed. The installation fails if you use small letters. You need to refer to pymysql as PyMySQL in your install commands in terminal. I don't know why.

Good luck!!! :+1:

Then the Seafile installer on Yuno continued to spit out all the same yellow errors as before despite the changes but nonetheless finished installing and seems to work.

Gilbog commented 2 years ago

Thanks for the new info, p1yn5ju6. I'm fairly inexperienced with Linux & servers (hence I use YunoHost :) Could you please post the exact commands that I need to use after I ssh as root into my YunoHost for

updating YunoHost (is it just apt update and then do System updates on the Yuno webadmin page?)
Installing PyMySQL

I'll probably manage with your help -- thanks in advance!

p1yn5ju6 commented 2 years ago

Hi!

I was signed in as root too… so no sudo (and, I think we’re in the same boat. I have been tinkering with linux and the idea of self hosting for a month)

I think the command was: apt install PyMySQL

I was definitely case sensitive. I couldn’t believe it when it made a difference.

Gilbog commented 2 years ago

Thanks!

I am updated to YunoHost 4.6.3.2 But when I run apt install PyMySQL I get Unable to locate package PyMySQL. Same error if I use all lowercase letters. Did you maybe run anything else?

BTW, I also just installed Nextcloud on my Raspberry Pi 4 YunoHost, it's been working fine so far (a few hours).

p1yn5ju6 commented 2 years ago

BTW, I also just installed Nextcloud on my Raspberry Pi 4 YunoHost, it's been working fine so far (a few hours).

Awesome! Welll done - resist the urge to tinker too much with it too much - I go all superstitious when Linux comes into thr equasion.

I am updated to YunoHost 4.6.3.2 But when I run apt install PyMySQL I get Unable to locate package PyMySQL. Same error if I use all lowercase letters. Did you maybe run anything else?

The answer in my head to this was: sigh probably... I feel like we are maybe the blind leading the blind here. However, I've just looked through my browser history to jog my memory as I've been plugging away at this server all weekend.

apt didnt work. the pip installer is what i used but had to install it.

So here's what i did:

apt install python3-pip

then

pip install PyMySQL

I was logged in as root so no need for sudo but you might need that.

Good luck - sorry for the slow reply.

Gilbog commented 2 years ago

Ha, ha, you said that very well: the blind leading the blind ... and it's us "beginners" with some technical curiosity who are actually the target group of YunoHost ...

Here's the latest news: I ran apt install python3-pip (also as user "root") and got python3-pip is already the newest version (18.1-5+rpt1), so nothing new got actually installed.

Then I ran pip install PyMySQL and I got -bash: pip: command not found

Go figure ... do you have any idea why?

p1yn5ju6 commented 2 years ago

Did you try the Seafile install again?

I’m wondering if I thought I was having a brain wave and fixed it with my own commands, but really, is it just that a diff app I installed between my Seafile installation attempts helped with prerequisites???

What I’ve just discovered is that even after a reboot my command history appears when I push the up arrow….

p1yn5ju6 commented 2 years ago

Right, here is every command I made, often just as stabs in the dark:

apt install PyMySQL

pip install PyMySQL python3 -m pip install PyMySQL

apt update

apt upgrade

pip install numpy

install pip

apt install pip conda create -n my-env apt install anaconda

conda install numpy

reboot

Some of these commands obvs didn't work but, I think the ones ive formatted as code did.

Then reboot and then install seafile.

If that doesn't work, is therw a way of giving you an image of my working config? I really don't know.

Gilbog commented 2 years ago

Ah, thanks, we're so similar in our approaches ... half we know something, half we try something, and in the process we (occasionally) blow up our installation. (I'm on the 4th YunoHost installation, currently). Nextcloud still works, BTW!

Of all the commands, only python3 -m pip install PyMySQL did something "real", all the others were either not recognized or did nothing that wasn't already installed or updated.

After rebooting I installed Seafile again via the webadmin page. The installation mostly worked "green" except these "yellow" errors:

pywavelets 1.2.0 has requirement numpy>=1.17.3, but you'll have numpy 1.16.2 which is incompatible.
scikit-image 0.19.1 has requirement numpy>=1.17.0, but you'll have numpy 1.16.2 which is incompatible.
scikit-image 0.19.1 has requirement scipy>=1.4.1, but you'll have scipy 1.1.0 which is incompatible.

After a looong time it finally successfully completed and Seafile shows up as a tile in the Yuno Portal and starts normally. (Ironically, since Nextcloud works on my YunoHost, I might not actually need it after all.)

Wooow. The two blind mice both made it, thanks to your persistence and creativity trying to get that PyMySQL installed -- you're my hero!

Thanks again, p1yn5ju6!

p1yn5ju6 commented 2 years ago

🥳🥳🥳 🎇🎇🎇

YAY!!!!

You have no idea how pleased I am. When I got your email alert, @Gilbog, I was elated. Team-work FTW! 🙌

I'm going to pour myself some cava to celebrate. I'm off ttomorrow, so why not??

It would be cool if someone in-the-know from the Yuno community could explain why a single line makes all ther difference.

lightnin commented 2 years ago

Same problem, Rpi 4, 4.3.6.3 (stable). https://paste.yunohost.org/raw/uhabihadih From above it looks like the install script is broken - shouldn't we set this package to broken in the directory then?

lightnin commented 2 years ago

If what the users above describe is correct, then the case of the name of the package "pymysql" in the following command on line 42 of /scripts/_common.sh is wrong, and needs to reflect the correct package case: PyMySQL.

I suppose this could cause the seafile package install to work for some users if another yunohost package has already installed PyMySQL. Easy fix @yalh76 ?

Line 42: sudo -u $seafile_user pip3 install --user --no-warn-script-location --upgrade future mysqlclient pymysql Pillow pylibmc captcha jinja2 sqlalchemy psd-tools django-pylibmc django-simple-captcha python3-ldap

yalh76 commented 2 years ago

If what the users above describe is correct, then the case of the name of the package "pymysql" in the following command on line 42 of /scripts/_common.sh is wrong, and needs to reflect the correct package case: PyMySQL.

I suppose this could cause the seafile package install to work for some users if another yunohost package has already installed PyMySQL. Easy fix @yalh76 ?

Line 42: sudo -u $seafile_user pip3 install --user --no-warn-script-location --upgrade future mysqlclient pymysql Pillow pylibmc captcha jinja2 sqlalchemy psd-tools django-pylibmc django-simple-captcha python3-ldap

No idea, I haven't worked on that part of the package, would be better to ask @Josue-T, his opinion about that

Josue-T commented 2 years ago

Hello,

Look like that sometime pip is case sensitive.

For the person who as this issue could you please try this procedure to check that all other packages are found (when pip is case sensitive):

python3 -m venv venv_test_install_python
source venv_test_install_python/bin/activate
pip3 install --upgrade future mysqlclient PyMySQL Pillow pylibmc captcha Jinja2 SQLAlchemy psd-tools django-pylibmc django-simple-captcha python3-ldap pycryptodome==3.12.0 cffi==1.14.0

lightnin commented 2 years ago

Hi @Josue-T - thanks for looking into this. Here's the result I get from the instructions above:

`(venv_test_install_python) admin@net:~ $ pip3 install --upgrade future mysqlclient PyMySQL Pillow pylibmc captcha Jinja2 SQLAlchemy psd-tools django-pylibmc django-simple-captcha python3-ldap pycryptodome==3.12.0 cffi==1.14.0 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple Collecting future Downloading https://www.piwheels.org/simple/future/future-0.18.2-py3-none-any.whl (491kB) 100% |████████████████████████████████| 491kB 866kB/s Collecting mysqlclient Downloading https://files.pythonhosted.org/packages/50/5f/eac919b88b9df39bbe4a855f136d58f80d191cfea34a3dcf96bf5d8ace0a/mysqlclient-2.1.1.tar.gz (88kB) 100% |████████████████████████████████| 92kB 2.6MB/s Complete output from command python setup.py egg_info: /bin/sh: 1: mysql_config: not found /bin/sh: 1: mariadb_config: not found /bin/sh: 1: mysql_config: not found mysql_config --version mariadb_config --version mysql_config --libs Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-_pl8nfom/mysqlclient/setup.py", line 15, in metadata, options = get_config() File "/tmp/pip-install-_pl8nfom/mysqlclient/setup_posix.py", line 70, in get_config libs = mysql_config("libs") File "/tmp/pip-install-_pl8nfom/mysqlclient/setup_posix.py", line 31, in mysql_config raise OSError("{} not found".format(_mysql_config_path)) OSError: mysql_config not found

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-_pl8nfom/mysqlclient/ `

Josue-T commented 2 years ago

Thankd for the feedback.

You need to install some dependences before to install the pip package with theses command:

apt install  python3 python3-setuptools python3-pip python3-requests python3-dev libmariadb-dev-compat libmariadb-dev   expect ffmpeg memcached libmemcached-dev  python3-scipy python3-matplotlib    libjpeg62-turbo-dev zlib1g-dev

And after can you try again ?

lightnin commented 2 years ago

(venv_test_install_python) admin@net:~ $ pip3 install --upgrade future mysqlclient PyMySQL Pillow pylibmc captcha Jinja2 SQLAlchemy psd-tools django-pylibmc django-simple-captcha python3-ldap pycryptodome==3.12.0 cffi==1.14.0 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple Collecting future Using cached https://www.piwheels.org/simple/future/future-0.18.2-py3-none-any.whl Collecting mysqlclient Using cached https://files.pythonhosted.org/packages/50/5f/eac919b88b9df39bbe4a855f136d58f80d191cfea34a3dcf96bf5d8ace0a/mysqlclient-2.1.1.tar.gz Collecting PyMySQL Downloading https://files.pythonhosted.org/packages/4f/52/a115fe175028b058df353c5a3d5290b71514a83f67078a6482cff24d6137/PyMySQL-1.0.2-py3-none-any.whl (43kB) 100% |████████████████████████████████| 51kB 2.8MB/s Collecting Pillow Downloading https://www.piwheels.org/simple/pillow/Pillow-9.2.0-cp37-cp37m-linux_armv7l.whl (809kB) 100% |████████████████████████████████| 819kB 510kB/s Collecting pylibmc Downloading https://www.piwheels.org/simple/pylibmc/pylibmc-1.6.1-cp37-cp37m-linux_armv7l.whl (88kB) 100% |████████████████████████████████| 92kB 3.3MB/s Collecting captcha Downloading https://files.pythonhosted.org/packages/11/b0/a5125b88c185586afc64ea6af894eab996de4ef28c395dcdf4a7818a9098/captcha-0.4-py3-none-any.whl (102kB) 100% |████████████████████████████████| 112kB 2.8MB/s Collecting Jinja2 Downloading https://files.pythonhosted.org/packages/bc/c3/f068337a370801f372f2f8f6bad74a5c140f6fda3d9de154052708dd3c65/Jinja2-3.1.2-py3-none-any.whl (133kB) 100% |████████████████████████████████| 133kB 2.7MB/s Collecting SQLAlchemy Downloading https://www.piwheels.org/simple/sqlalchemy/SQLAlchemy-1.4.39-cp37-cp37m-linux_armv7l.whl (1.6MB) 100% |████████████████████████████████| 1.6MB 274kB/s Collecting psd-tools Downloading https://www.piwheels.org/simple/psd-tools/psd_tools-1.9.21-cp37-cp37m-linux_armv7l.whl (261kB) 100% |████████████████████████████████| 266kB 1.4MB/s Collecting django-pylibmc Downloading https://files.pythonhosted.org/packages/1b/2b/cbc55be77062f783b2a28dcc0aa6bb8f55ebbbf2c186b76e58ea79e25ee5/django_pylibmc-0.6.1-py2.py3-none-any.whl Collecting django-simple-captcha Downloading https://files.pythonhosted.org/packages/5c/2b/e7dd7a1c772f722c1fecd0dac495e9a19499cd94677fb3c2e689bccbd289/django_simple_captcha-0.5.17-py2.py3-none-any.whl (93kB) 100% |████████████████████████████████| 102kB 3.3MB/s Collecting python3-ldap Downloading https://files.pythonhosted.org/packages/5a/ee/98e445349b4c5296b41798719dd681195beb3550336090a399ab236527e7/python3_ldap-0.9.8.4-py2.py3-none-any.whl (295kB) 100% |████████████████████████████████| 296kB 1.1MB/s Collecting pycryptodome==3.12.0 Downloading https://files.pythonhosted.org/packages/dd/3b/38d83c2725fec5b837fc05d5c6e0178a420ff839a6ad5872f10c89244899/pycryptodome-3.12.0.zip (3.7MB) 100% |████████████████████████████████| 3.7MB 117kB/s Collecting cffi==1.14.0 Downloading https://www.piwheels.org/simple/cffi/cffi-1.14.0-cp37-cp37m-linux_armv7l.whl (344kB) 100% |████████████████████████████████| 348kB 1.1MB/s Collecting MarkupSafe>=2.0 (from Jinja2) Downloading https://www.piwheels.org/simple/markupsafe/MarkupSafe-2.1.1-cp37-cp37m-linux_armv7l.whl Collecting importlib-metadata; python_version < "3.8" (from SQLAlchemy) Downloading https://files.pythonhosted.org/packages/d2/a2/8c239dc898138f208dd14b441b196e7b3032b94d3137d9d8453e186967fc/importlib_metadata-4.12.0-py3-none-any.whl Collecting scipy (from psd-tools) Downloading https://www.piwheels.org/simple/scipy/scipy-1.7.3-cp37-cp37m-linux_armv7l.whl (65.5MB) 100% |████████████████████████████████| 65.5MB 6.6kB/s Collecting attrs>=19.2.0 (from psd-tools) Downloading https://files.pythonhosted.org/packages/be/be/7abce643bfdf8ca01c48afa2ddf8308c2308b0c3b239a44e57d020afa0ef/attrs-21.4.0-py2.py3-none-any.whl (60kB) 100% |████████████████████████████████| 61kB 3.1MB/s Collecting aggdraw (from psd-tools) Downloading https://files.pythonhosted.org/packages/63/90/8cabdc73526cd8628ddb124e2e55f77dc3324bdddccc3dd14d070076bb19/aggdraw-1.3.15.tar.gz (260kB) 100% |████████████████████████████████| 266kB 1.1MB/s Collecting scikit-image (from psd-tools) Downloading https://www.piwheels.org/simple/scikit-image/scikit_image-0.19.3-cp37-cp37m-linux_armv7l.whl (16.9MB) 100% |████████████████████████████████| 16.9MB 25kB/s Collecting docopt>=0.5 (from psd-tools) Downloading https://www.piwheels.org/simple/docopt/docopt-0.6.2-py2.py3-none-any.whl Collecting numpy (from psd-tools) Downloading https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (10.3MB) 100% |████████████████████████████████| 10.3MB 43kB/s Installing build dependencies ... done Collecting Django>=2.2 (from django-simple-captcha) Downloading https://files.pythonhosted.org/packages/c3/68/b63abc009adee25c1bd266b3740e173eab656608cf21641594a37e02cf57/Django-3.2.13-py3-none-any.whl (7.9MB) 100% |████████████████████████████████| 7.9MB 59kB/s Collecting django-ranged-response==0.2.0 (from django-simple-captcha) Downloading https://www.piwheels.org/simple/django-ranged-response/django_ranged_response-0.2.0-py3-none-any.whl Collecting pyasn1>=0.1.7 (from python3-ldap) Downloading https://files.pythonhosted.org/packages/62/1e/a94a8d635fa3ce4cfc7f506003548d0a2447ae76fd5ca53932970fe3053f/pyasn1-0.4.8-py2.py3-none-any.whl (77kB) 100% |████████████████████████████████| 81kB 2.3MB/s Collecting pycparser (from cffi==1.14.0) Downloading https://files.pythonhosted.org/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118kB) 100% |████████████████████████████████| 122kB 3.1MB/s Collecting typing-extensions>=3.6.4; 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error: invalid command 'bdist_wheel'

Failed building wheel for mysqlclient Running setup.py clean for mysqlclient Running setup.py bdist_wheel for pycryptodome ... error Complete output from command /home/admin/venv_test_install_python/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-install-y01lq71m/pycryptodome/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/pip-wheel-1j72yjp3 --python-tag cp37: Testing support for clang Target does not support clang Testing support for gcc Target does support gcc Testing support for stdint.h header Target does support stdint.h header Testing support for 128-bit integer Target does not support 128-bit integer Testing support for cpuid.h header Target does not support cpuid.h header Testing support for intrin.h header Target does not support intrin.h header Testing support for posix_memalign Target does support posix_memalign Testing support for SSE2(intrin.h) Target does not support SSE2(intrin.h) Testing support for SSE2(x86intrin.h) Target does not support SSE2(x86intrin.h) Testing support for SSE2(emmintrin.h) Target does not support SSE2(emmintrin.h) Testing support for gcc Target does support gcc Warning: compiler does not support AESNI instructions Warning: compiler does not support CLMUL instructions usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: -c --help [cmd1 cmd2 ...] or: -c --help-commands or: -c cmd --help

error: invalid command 'bdist_wheel'

Failed building wheel for pycryptodome Running setup.py clean for pycryptodome Running setup.py bdist_wheel for aggdraw ... error Complete output from command /home/admin/venv_test_install_python/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-install-y01lq71m/aggdraw/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/pip-wheel-v2ut6kr0 --python-tag cp37: Trying freetype-config to find freetype library... Using ctypes to find freetype library... Trying 'pkgconfig' to find freetype library... === freetype not available usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: -c --help [cmd1 cmd2 ...] or: -c --help-commands or: -c cmd --help

error: invalid command 'bdist_wheel'

Failed building wheel for aggdraw Running setup.py clean for aggdraw Running setup.py bdist_wheel for numpy ... |client_loop: send disconnect: Broken pipe

Josue-T commented 2 years ago

Thanks,

You might need to install this missing dependancy with this command:

apt install python3-wheel

lightnin commented 2 years ago

Nope, it was already in there: (venv_test_install_python) admin@net:~ $ sudo apt install python3-wheel Reading package lists... Done Building dependency tree
Reading state information... Done python3-wheel is already the newest version (0.32.3-2). python3-wheel set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. (venv_test_install_python) admin@net:~ $

Josue-T commented 2 years ago

Hello,

I think there are an issue to find the wheel package from the venv. Can you try again with a specific user with theses commands:

apt install  python3 python3-setuptools python3-pip python3-requests python3-dev libmariadb-dev-compat libmariadb-dev   expect ffmpeg memcached libmemcached-dev  python3-scipy python3-matplotlib    libjpeg62-turbo-dev zlib1g-dev
useradd test_pip_seafile
su test_pip_seafile
pip3 install --user --upgrade future mysqlclient PyMySQL Pillow pylibmc captcha Jinja2 SQLAlchemy psd-tools django-pylibmc django-simple-captcha python3-ldap pycryptodome==3.12.0 cffi==1.14.0
userdel test_pip_seafile

lightnin commented 2 years ago

Well I ran into too many problems I'm afraid - I don't yet understand how venvs and apt interact (Can certain packages be installed in a venv via apt, or is apt always global for the system?) So perhaps there's another way to test if this issue is due to case sensitivity of packages in pip. Perhaps it would make sense to submit a PR against the install with the correct case for the packages, since the correct case is unlikely to introduce any problems. Unfortunately it's a bit over my head.

Josue-T commented 2 years ago

Well, seafile dont use venv to install packages. We just use a speific user to install the package. I sugested to use venv because it might ne an easyest way to test but it was not the case.

lightnin commented 2 years ago

The issue is that the created user doesn't have the privileges necessary to install the files. Which would then mean I'd have to add them to the sudo list to run the command. And this is my production system and I don't want to mess it up.

Josue-T commented 1 year ago

Hello, can you test again from the testing branch. I pushed a fix about this.

lightnin commented 1 year ago

Unfortunately I'm not sure how to test a yunohost app install from the testing branch. Should i install from command line and pass the raw url of the testing branch as an argument? I'm also away from my machine for the next month and a bit concerned I might need physical access... Is @p1yn5ju6 available to give it a try?

matthiasbe commented 1 year ago

Hi, I add the same issue just today, on version 11.0.11 of yunohost. Logs: https://paste.yunohost.org/raw/qekabigadi

I'm using Raspberry Pi 3B+

After executing sudo pip3 install pymysql installation went through without issue

Pfeil commented 5 months ago

I also met the issue today and can confirm sudo pip3 install pymysql did the trick.

Yunohost 11.2.10 (stable, 64bit) Raspberry Pi 4

YunoHost-Apps / seafile_ynh