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#1 2024-02-14 11:12:43
- Frankwarch
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- Registered: 2024-02-12
- Posts: 36
Undefined symbol libgssapi_krb5.so.2
I've been trying to use the package anki to try to learn languages. Installed the bin from the AUR and then installed all the dependencies required via pip. When I try to run anki, I get the following message:
anki
Traceback (most recent call last):
File "/home/frank/.miniconda3/bin/anki", line 5, in <module>
from aqt import run
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/__init__.py", line 52, in <module>
from aqt import gui_hooks
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/gui_hooks.py", line 11, in <module>
from _aqt.hooks import *
File "/home/frank/.miniconda3/lib/python3.11/site-packages/_aqt/hooks.py", line 18, in <module>
from aqt.qt import QDialog, QEvent, QMenu, QModelIndex, QWidget, QMimeData
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/qt/__init__.py", line 20, in <module>
from .qt6 import *
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/qt/qt6.py", line 16, in <module>
from PyQt6.QtNetwork import QLocalServer, QLocalSocket, QNetworkProxy
ImportError: /usr/lib/libgssapi_krb5.so.2: undefined symbol: k5_buf_cstring, version krb5support_0_MITSeems related to this post, but my libraries seem to be installed in the right place (perhaps I'm wrong, I'm new to arch and linux in general). When I run ldd I get the following:
ldd /usr/lib/libgssapi_krb5.so.2
linux-vdso.so.1 (0x00007ffcc27d3000)
libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0x0000787c039e4000)
libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0x0000787c039b6000)
libcom_err.so.2 => /usr/lib/libcom_err.so.2 (0x0000787c039b0000)
libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0x0000787c039a2000)
libkeyutils.so.1 => /usr/lib/libkeyutils.so.1 (0x0000787c0399b000)
libresolv.so.2 => /usr/lib/libresolv.so.2 (0x0000787c0398a000)
libc.so.6 => /usr/lib/libc.so.6 (0x0000787c037a6000)
/usr/lib64/ld-linux-x86-64.so.2 (0x0000787c03b3f000)Any suggestions? I really have no clue on what is happening. Help would be much appreciated.
Last edited by Frankwarch (2024-02-14 11:13:27)
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#2 2024-02-14 14:25:31
- Scimmia
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Re: Undefined symbol libgssapi_krb5.so.2
start with `pacman -Q krb5`
But both files are from that package, so everything should be in sync. You realize that you're not running anything from a package there, right? Everything is from miniconda, including anki itself. If you're using an AUR package, why are you using miniconda and pip?
Last edited by Scimmia (2024-02-14 14:28:05)
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#3 2024-02-14 16:44:16
- Frankwarch
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Re: Undefined symbol libgssapi_krb5.so.2
I get the following:
pacman -Q krb5
krb5 1.21.2-2I installed things with pip because they were Python libraries. I did not install anki with pip, however. Should I have installed the rest a different way?
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#4 2024-02-14 16:46:45
- seth
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- Posts: 74,325
Re: Undefined symbol libgssapi_krb5.so.2
https://aur.archlinux.org/packages/anki drags in all the python you need, no pip involved.
pacman -Qikk anki
stat /usr/lib/libkrb5support.so.0
readelf -sW /usr/lib/libkrb5support.so.0 | grep k5_buf_cstring
pacman -Qikk krb5
LD_PRELOAD=/usr/lib/libkrb5support.so.0 ankiOffline
#5 2024-02-14 16:51:18
- Scimmia
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Re: Undefined symbol libgssapi_krb5.so.2
Python things can be packaged, too. That's how packages work, they have dependencies on things they need, once you install the package, everything should be there. It probably didn't for you because you're completely overriding the system python, breaking pretty much anything packaged that uses python. You activate miniconda specifically when you want it, don't use it at all times.
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#6 2024-02-14 16:54:26
- Frankwarch
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Re: Undefined symbol libgssapi_krb5.so.2
Okay, then should I deactivate miniconda? How do I do it? Sorry, I really don't have much experience with these kinds of things.
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#7 2024-02-14 16:55:55
- Scimmia
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Re: Undefined symbol libgssapi_krb5.so.2
Why are you using it at all?
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#8 2024-02-14 17:03:47
- Frankwarch
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Re: Undefined symbol libgssapi_krb5.so.2
Probably needed some python dependency for some other library and it was an easy way to install it... I really don't know another one.
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#9 2024-02-14 17:06:38
- seth
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Re: Undefined symbol libgssapi_krb5.so.2
If you've installed anki as AUR package, why's there "/home/frank/.miniconda3/bin/anki"?
Post the outputs of the commands in #4 and also
type -a ankiOffline
#10 2024-02-14 17:12:46
- Frankwarch
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Re: Undefined symbol libgssapi_krb5.so.2
I don't know why it creates a file there, maybe because it uses a lot of Python dependencies?. The results are:
1
pacman -Qikk anki
Name : anki-bin
Version : 23.12.1-1
Description : Helps you remember facts (like words/phrases in a foreign
language) efficiently. Installed with wheel.
Architecture : x86_64
URL : https://apps.ankiweb.net/
Licenses : AGPL3
Groups : None
Provides : anki=23.12.1
Depends On : python-beautifulsoup4 python-requests python-flask
python-flask-cors python-jsonschema python-pyqt6
python-pyqt6-webengine python-send2trash python-waitress
python-decorator python-distro python-markdown
python-orjson python-protobuf python-pysocks qt6-svg
Optional Deps : lame: record sound [installed]
mpv: play sound. prefered over mplayer [installed]
mplayer: play sound
Required By : None
Optional For : None
Conflicts With : anki
Replaces : None
Installed Size : 60.91 MiB
Packager : Unknown Packager
Build Date : Wed 14 Feb 2024 06:08:32 PM CET
Install Date : Wed 14 Feb 2024 06:09:18 PM CET
Install Reason : Explicitly installed
Install Script : No
Validated By : None
warning: anki-bin: /home/frank (UID mismatch)
warning: anki-bin: /home/frank (GID mismatch)
warning: anki-bin: /home/frank (Permissions mismatch)
warning: anki-bin: /home/frank/.miniconda3 (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3 (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/bin (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/bin (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11 (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11 (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11/site-packages (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11/site-packages (GID mismatch)
anki-bin: 1237 total files, 6 altered files2
stat /usr/lib/libkrb5support.so.0
File: /usr/lib/libkrb5support.so.0 -> libkrb5support.so.0.1
Size: 21 Blocks: 0 IO Block: 4096 symbolic link
Device: 259,7 Inode: 15218165 Links: 1
Access: (0777/lrwxrwxrwx) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2024-02-13 19:53:38.727043799 +0100
Modify: 2023-12-24 08:55:18.000000000 +0100
Change: 2024-02-12 19:52:42.696475059 +0100
Birth: 2024-02-12 19:36:31.659768032 +01003
readelf -sW /usr/lib/libkrb5support.so.0 | grep k5_buf_cstring
126: 00000000000053d0 90 FUNC GLOBAL DEFAULT 11 k5_buf_cstring@@krb5support_0_MIT4
pacman -Qikk krb5
Name : krb5
Version : 1.21.2-2
Description : The Kerberos network authentication system
Architecture : x86_64
URL : https://web.mit.edu/kerberos/
Licenses : custom
Groups : None
Provides : libgssapi_krb5.so=2-64 libgssrpc.so=4-64
libk5crypto.so=3-64 libkadm5clnt_mit.so=12-64
libkadm5srv_mit.so=12-64 libkdb5.so=10-64
libkdb_ldap.so=1-64 libkrad.so=0-64 libkrb5.so=3-64
libkrb5support.so=0-64
Depends On : glibc e2fsprogs libldap keyutils libverto-module-base
libkeyutils.so=1-64 libss.so=2-64 libcom_err.so=2-64
libverto.so=1-64
Optional Deps : None
Required By : audit cifs-utils curl evolution-data-server lib32-krb5
libsoup libsoup3 libtirpc openssh postgresql-libs
qt6-base
Optional For : None
Conflicts With : None
Replaces : None
Installed Size : 4.62 MiB
Packager : Antonio Rojas <arojas@archlinux.org>
Build Date : Sun 24 Dec 2023 08:55:18 AM CET
Install Date : Mon 12 Feb 2024 07:36:31 PM CET
Install Reason : Installed as a dependency for another package
Install Script : No
Validated By : Signature
krb5: 204 total files, 0 altered files5
LD_PRELOAD=/usr/lib/libkrb5support.so.0 anki
Traceback (most recent call last):
File "/home/frank/.miniconda3/bin/anki", line 5, in <module>
from aqt import run
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/__init__.py", line 52, in <module>
from aqt import gui_hooks
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/gui_hooks.py", line 11, in <module>
from _aqt.hooks import *
File "/home/frank/.miniconda3/lib/python3.11/site-packages/_aqt/hooks.py", line 18, in <module>
from aqt.qt import QDialog, QEvent, QMenu, QModelIndex, QWidget, QMimeData
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/qt/__init__.py", line 20, in <module>
from .qt6 import *
File "/home/frank/.miniconda3/lib/python3.11/site-packages/aqt/qt/qt6.py", line 16, in <module>
from PyQt6.QtNetwork import QLocalServer, QLocalSocket, QNetworkProxy
ImportError: /home/frank/.miniconda3/bin/../lib/./libcom_err.so.3: undefined symbol: krb5int_strlcpy, version krb5support_0_MIT6
type -a anki
anki is /home/frank/.miniconda3/bin/anki
anki is /usr/bin/anki
anki is /home/frank/.miniconda3/bin/ankiLast edited by Frankwarch (2024-02-14 17:13:30)
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#11 2024-02-14 17:20:48
- seth
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- Registered: 2012-09-03
- Posts: 74,325
Re: Undefined symbol libgssapi_krb5.so.2
Name : anki-binwarning: anki-bin: /home/frank (UID mismatch)
warning: anki-bin: /home/frank (GID mismatch)
warning: anki-bin: /home/frank (Permissions mismatch)
warning: anki-bin: /home/frank/.miniconda3 (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3 (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/bin (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/bin (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11 (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11 (GID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11/site-packages (UID mismatch)
warning: anki-bin: /home/frank/.miniconda3/lib/python3.11/site-packages (GID mismatch)
anki-bin: 1237 total files, 6 altered filesHow *exactly* did you install that?
Did you set the pkgdir to ~/.miniconda3 ???
LD_PRELOAD=/usr/lib/libkrb5support.so.0 shifts to the next symbol mismatch, so what's in ~/.miniconda3/lib ?
ls -lR ~/.miniconda3/libAnd more importantly: why?
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#12 2024-02-14 17:25:35
- Scimmia
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Re: Undefined symbol libgssapi_krb5.so.2
By overriding the system python while building the package, you have created a huge mess. When calling python -m installer, it called the miniconda version and everything ended up wrong.
Dump miniconda completely. Get rid of any configs that activate it, get rid of it from $PATH if you did anything there. Then start over with rebuilding the package.
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#13 2024-02-14 17:27:10
- Frankwarch
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- Registered: 2024-02-12
- Posts: 36
Re: Undefined symbol libgssapi_krb5.so.2
To install it I just used trizen -S anki-bin... I did not edit the PKGBUILD at all. Perhaps I can reinstall and set it manually?
The output of ls -lR ~/.miniconda3/lib is way too long to post here... A normal ls yields
ls .miniconda3/lib
cmake libicudata.a libpcre2-16.a
engines-3 libicudata.so libpcre2-16.so
icu libicudata.so.73 libpcre2-16.so.0
itcl4.2.2 libicudata.so.73.1 libpcre2-16.so.0.11.2
krb5 libicui18n.a libpcre2-32.a
ossl-modules libicui18n.so libpcre2-32.so
pkgconfig libicui18n.so.73 libpcre2-32.so.0
python3.1 libicui18n.so.73.1 libpcre2-32.so.0.11.2
python3.11 libicuio.a libpcre2-8.a
sqlite3.36.0 libicuio.so libpcre2-8.so
tcl8 libicuio.so.73 libpcre2-8.so.0
tcl8.6 libicuio.so.73.1 libpcre2-8.so.0.11.2
tdbc1.1.3 libicutest.a libpcre2-posix.a
tdbcmysql1.1.3 libicutest.so libpcre2-posix.so
tdbcodbc1.1.3 libicutest.so.73 libpcre2-posix.so.3
tdbcpostgres1.1.3 libicutest.so.73.1 libpcre2-posix.so.3.0.4
terminfo libicutu.a libpython3.11.so
thread2.8.7 libicutu.so libpython3.11.so.1.0
tk8.6 libicutu.so.73 libpython3.so
libarchive.a libicutu.so.73.1 libquadmath.so
libarchive.so libicuuc.a libquadmath.so.0
libarchive.so.19 libicuuc.so libquadmath.so.0.0.0
libasan.so libicuuc.so.73 libreadline.a
libasan.so.6 libicuuc.so.73.1 libreadline.so
libasan.so.6.0.0 libitm.so libreadline.so.8
libatomic.so libitm.so.1 libreadline.so.8.2
libatomic.so.1 libitm.so.1.0.0 libreproc++.so
libatomic.so.1.2.0 libk5crypto.so libreproc.so
libbz2.a libk5crypto.so.3 libreproc++.so.14
libbz2.so libk5crypto.so.3.1 libreproc.so.14
libbz2.so.1.0 libkadm5clnt_mit.so libreproc++.so.14.2.4
libbz2.so.1.0.8 libkadm5clnt_mit.so.12 libreproc.so.14.2.4
libcares.so libkadm5clnt_mit.so.12.0 libsolvext.so
libcares.so.2 libkadm5clnt.so libsolvext.so.1
libcares.so.2.6.1 libkadm5srv_mit.so libsolv.so
libcom_err.so libkadm5srv_mit.so.12 libsolv.so.1
libcom_err.so.3 libkadm5srv_mit.so.12.0 libsqlite3.so
libcom_err.so.3.0 libkadm5srv.so libsqlite3.so.0
libcrypto.a libkdb5.so libsqlite3.so.0.8.6
libcrypto.so libkdb5.so.10 libssh2.a
libcrypto.so.3 libkdb5.so.10.0 libssh2.so
libcurl.so libkrad.so libssh2.so.1
libcurl.so.4 libkrad.so.0 libssh2.so.1.0.1
libcurl.so.4.8.0 libkrad.so.0.0 libssl.a
libedit.a libkrb5.so libssl.so
libedit.so libkrb5.so.3 libssl.so.3
libedit.so.0 libkrb5.so.3.3 libstdc++.so
libedit.so.0.0.72 libkrb5support.so libstdc++.so.6
libev.so libkrb5support.so.0 libstdc++.so.6.0.29
libev.so.4 libkrb5support.so.0.1 libtcl8.6.so
libev.so.4.0.0 liblsan.so libtclstub8.6.a
libffi.7.so liblsan.so.0 libtinfo.a
libffi.8.so liblsan.so.0.0.0 libtinfo.so
libffi.a liblz4.so libtinfo.so.6
libffi.so liblz4.so.1 libtinfo.so.6.4
libffi.so.7 liblz4.so.1.9.4 libtinfow.a
libffi.so.8 liblzma.a libtinfow.so
libffi.so.8.1.2 liblzma.so libtinfow.so.6
libfmt.so liblzma.so.5 libtinfow.so.6.4
libfmt.so.9 liblzma.so.5.4.5 libtk8.6.so
libfmt.so.9.1.0 libmamba.so libtkstub8.6.a
libform.a libmamba.so.2 libtsan.so
libform.so libmamba.so.2.0.0 libtsan.so.0
libform.so.6 libmenu.a libtsan.so.0.0.0
libform.so.6.4 libmenu.so libubsan.so
libformw.a libmenu.so.6 libubsan.so.1
libformw.so libmenu.so.6.4 libubsan.so.1.0.0
libformw.so.6 libmenuw.a libuuid.a
libformw.so.6.4 libmenuw.so libuuid.so
libgcc_s.so libmenuw.so.6 libuuid.so.1
libgcc_s.so.1 libmenuw.so.6.4 libuuid.so.1.3.0
libgmock_main.so libncurses++.a libverto.so
libgmock_main.so.1.11.0 libncurses.a libverto.so.0
libgmock.so libncurses.so libverto.so.0.0
libgmock.so.1.11.0 libncurses.so.6 libxml2.so
libgomp.so libncurses.so.6.4 libxml2.so.2
libgomp.so.1 libncurses++w.a libxml2.so.2.10.4
libgomp.so.1.0.0 libncursesw.a libyaml-cpp.so
libgssapi_krb5.so libncursesw.so libyaml-cpp.so.0.8
libgssapi_krb5.so.2 libncursesw.so.6 libyaml-cpp.so.0.8.0
libgssapi_krb5.so.2.2 libncursesw.so.6.4 libz.a
libgssrpc.so libnghttp2.so libz.so
libgssrpc.so.4 libnghttp2.so.14 libz.so.1
libgssrpc.so.4.2 libnghttp2.so.14.25.0 libz.so.1.2.13
libgtest_main.so libpanel.a libzstd.a
libgtest_main.so.1.11.0 libpanel.so libzstd.so
libgtest.so libpanel.so.6 libzstd.so.1
libgtest.so.1.11.0 libpanel.so.6.4 libzstd.so.1.5.5
libhistory.a libpanelw.a tclConfig.sh
libhistory.so libpanelw.so tclooConfig.sh
libhistory.so.8 libpanelw.so.6 tkConfig.sh
libhistory.so.8.2 libpanelw.so.6.4Should I post the results of using -lR anyway?
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#14 2024-02-14 17:35:28
- Frankwarch
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- Registered: 2024-02-12
- Posts: 36
Re: Undefined symbol libgssapi_krb5.so.2
Dump miniconda completely. Get rid of any configs that activate it, get rid of it from $PATH if you did anything there. Then start over with rebuilding the package.
I really don't know how to do this safely... How should I proceed? At least with removing it. My $PATH is the following:
/home/frank/.miniconda3/bin:/home/frank/.miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/frank/scripts:/home/frank/.local/bin:/home/frank/.config/emacs/bin:/home/frank/.miniconda3/binLast edited by Frankwarch (2024-02-14 17:36:04)
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#15 2024-02-14 18:09:14
- loqs
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- Registered: 2014-03-06
- Posts: 18,859
Re: Undefined symbol libgssapi_krb5.so.2
How did you install miniconda?
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#16 2024-02-14 18:16:10
- Frankwarch
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- Registered: 2024-02-12
- Posts: 36
Re: Undefined symbol libgssapi_krb5.so.2
I don't remember exactly, but I think it was something like this: https://waylonwalker.com/install-miniconda/
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#17 2024-02-14 20:19:48
- Scimmia
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Re: Undefined symbol libgssapi_krb5.so.2
I'm on my phone so I'm not going to look it up, but you need to figure out what those conda init commands did and undo them.
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