Can't use calibre

Nice, Thank you very much. I still need to uninstall and reboot the system. Hopefully it is going to fix it.

I can’t gloss over this. You should never run yay as sudo. It’s just yay.

I’ve installed it from the repos dozens of times without issue. I’d rarely suggest getting it directly from a website as they almost never work with Arch.

I’d recommend the flatpak version if you’re still having issues. It’s been around forever and hasn’t changed much.

2 Likes

Unfortunately it didn’t work, I had to install the binary directly from the link below and it is working now. I wonder if there is an issue in the system tho.

That is certainly very strange. I have been running calibre from the official repo with 0 problems ever since I started using linux.

Maybe you should run sudo find / -wholename "*libxml2*" to see what other libxml2 packages are installed on your system. I mean just to further diagnose the issue.

I know you managed to get calibre to work, but this whole problem could be a sign of a deeper issue and is worth investigating.

1 Like

It didn’t work as in you encountered the same error message when you use calibre?

I checked pactree python-lxml and pactree python-html5-parser and both of those packages require libxml2 to work. And since python-lxml and python-html5-parser are required by calibre, pacman should resolve all these dependencies and the correct version of libxml2 will be installed if it hasn’t been installed already.

The latest version of libxml2 in the repo is 2.10.3, so where did libxml2 version 2.9.14 even come from?

1 Like

Yes, same error.

I have no idea where it is coming from. maybe another app uses it too. I did removed Calibre with pacman -Rns tho, so there should be no more of this package anymore. I have tried my best to not install anything out of repository. Just few necessary packages form AUR. So I am not sure even it is my fault or it is an issue with pacman.

I totally agree, let me try the command you just mentioned.

here is the result of that search, it is interesting other timeshift files that shows the location on it before uninstall it founds some current files still:

❯ sudo find / -wholename "*libxml2*"
[sudo] password for arash:
Sorry, try again.
[sudo] password for arash:
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/share/licenses/libxml2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/share/licenses/libxml2/Copyright
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/share/licenses/lib32-libxml2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/share/licenses/lib32-libxml2/Copyright
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/share/doc/xmlsec1/images/libxml2-logo.png
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib32/libxml2.so
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib32/libxml2.so.2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib32/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib32/cmake/libxml2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib32/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/chvalid.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlerror.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlschemas.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/encoding.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/SAX.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlversion.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/uri.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlexports.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/HTMLtree.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/valid.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlmemory.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlstring.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/hash.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/nanohttp.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/globals.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/parser.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/threads.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/schematron.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xinclude.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlmodule.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlIO.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xpathInternals.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xlink.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xpath.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/entities.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlsave.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlregexp.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/schemasInternals.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/SAX2.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlreader.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xpointer.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlschemastypes.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/catalog.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/HTMLparser.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/list.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/tree.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/relaxng.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlunicode.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/debugXML.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/pattern.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/nanoftp.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/parserInternals.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlautomata.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/xmlwriter.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/c14n.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/include/libxml2/libxml/dict.h
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/drv_libxml2.py
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/libxml2mod.so
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/libxml2.py
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/libxml2.so
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/libxml2.so.2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/girepository-1.0/libxml2-2.0.typelib
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/cmake/libxml2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/usr/lib/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/libxml2-2.10.3-2
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-11-28_10-52-48/localhost/var/lib/pacman/local/libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/share/licenses/libxml2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/share/licenses/libxml2/Copyright
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/share/licenses/lib32-libxml2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/share/licenses/lib32-libxml2/Copyright
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/share/doc/xmlsec1/images/libxml2-logo.png
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib32/libxml2.so
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib32/libxml2.so.2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib32/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib32/cmake/libxml2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib32/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/chvalid.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlerror.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlschemas.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/encoding.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/SAX.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlversion.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/uri.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlexports.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/HTMLtree.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/valid.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlmemory.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlstring.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/hash.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/nanohttp.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/globals.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/parser.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/threads.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/schematron.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xinclude.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlmodule.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlIO.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xpathInternals.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xlink.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xpath.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/entities.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlsave.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlregexp.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/schemasInternals.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/SAX2.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlreader.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xpointer.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlschemastypes.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/catalog.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/HTMLparser.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/list.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/tree.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/relaxng.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlunicode.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/debugXML.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/pattern.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/nanoftp.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/parserInternals.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlautomata.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/xmlwriter.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/c14n.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/include/libxml2/libxml/dict.h
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/drv_libxml2.py
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/libxml2mod.so
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/libxml2.py
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/libxml2.so
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/libxml2.so.2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/girepository-1.0/libxml2-2.0.typelib
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/cmake/libxml2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/usr/lib/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-12-02_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/share/licenses/libxml2
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/share/licenses/libxml2/Copyright
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/share/licenses/lib32-libxml2
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/share/licenses/lib32-libxml2/Copyright
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/share/doc/xmlsec1/images/libxml2-logo.png
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/lib32/libxml2.so
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/lib32/libxml2.so.2
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/lib32/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/lib32/cmake/libxml2
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/lib32/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/chvalid.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/xmlerror.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/xmlschemas.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/encoding.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/SAX.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/xmlversion.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/uri.h
/home/timeshift/snapshots/2022-11-30_12-00-06/localhost/usr/include/libxml2/libxml/xmlexports.h
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/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/include/libxml2/libxml/xmlwriter.h
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/include/libxml2/libxml/c14n.h
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/include/libxml2/libxml/dict.h
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/drv_libxml2.py
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/libxml2mod.so
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/libxml2.py
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/libxml2.so
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/libxml2.so.2
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/girepository-1.0/libxml2-2.0.typelib
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/cmake/libxml2
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/usr/lib/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/libxml2-2.10.3-2
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-11-29_12-00-13/localhost/var/lib/pacman/local/libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/share/licenses/libxml2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/share/licenses/libxml2/Copyright
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/share/licenses/lib32-libxml2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/share/licenses/lib32-libxml2/Copyright
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/share/doc/xmlsec1/images/libxml2-logo.png
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib32/libxml2.so
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib32/libxml2.so.2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib32/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib32/cmake/libxml2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib32/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/chvalid.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlerror.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlschemas.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/encoding.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/SAX.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlversion.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/uri.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlexports.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/HTMLtree.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/valid.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlmemory.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlstring.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/hash.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/nanohttp.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/globals.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/parser.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/threads.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/schematron.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xinclude.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlmodule.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlIO.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xpathInternals.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xlink.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xpath.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/entities.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlsave.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlregexp.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/schemasInternals.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/SAX2.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlreader.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xpointer.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlschemastypes.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/catalog.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/HTMLparser.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/list.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/tree.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/relaxng.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlunicode.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/debugXML.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/pattern.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/nanoftp.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/parserInternals.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlautomata.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/xmlwriter.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/c14n.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/include/libxml2/libxml/dict.h
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/drv_libxml2.py
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/libxml2mod.so
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/libxml2.py
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.pyc
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.opt-1.pyc
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/libxml2.so
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/libxml2.so.2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/girepository-1.0/libxml2-2.0.typelib
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/libxml2.so.2.10.3
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/cmake/libxml2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/usr/lib/cmake/libxml2/libxml2-config.cmake
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/lib32-libxml2-2.10.3-2/desc
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2/mtree
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2/files
/home/timeshift/snapshots/2022-11-28_12-00-02/localhost/var/lib/pacman/local/libxml2-2.10.3-2/desc
/home/arash/arashafile/ariroot/applications/backlog/01-AppPortable/Gajim 1.4/Gajim/bin/libxml2-2.dll
/home/arash/arashafile/ariroot/applications/backlog/01-AppPortable/Gajim 1.4/Gajim/lib/python3.9/site-packages/drv_libxml2.pyc
/home/arash/arashafile/ariroot/applications/backlog/01-AppPortable/Gajim 1.4/Gajim/lib/python3.9/site-packages/libxml2mod.pyd
/home/arash/arashafile/ariroot/applications/backlog/01-AppPortable/Gajim 1.4/Gajim/lib/python3.9/site-packages/libxml2.pyc
/home/arash/arashafile/ariroot/applications/backlog/01-AppPortable/Gajim 1.4/Gajim/lib/girepository-1.0/libxml2-2.0.typelib
find: ‘/tmp/.mount_EspansTLNWf0’: Permission denied
find: ‘/tmp/.mount_EspansRQptbc’: Permission denied
/var/lib/pacman/local/libxml2-2.10.3-2
/var/lib/pacman/local/libxml2-2.10.3-2/desc
/var/lib/pacman/local/libxml2-2.10.3-2/files
/var/lib/pacman/local/libxml2-2.10.3-2/mtree
/var/lib/pacman/local/lib32-libxml2-2.10.3-2
/var/lib/pacman/local/lib32-libxml2-2.10.3-2/desc
/var/lib/pacman/local/lib32-libxml2-2.10.3-2/files
/var/lib/pacman/local/lib32-libxml2-2.10.3-2/mtree
/var/cache/pacman/pkg/lib32-libxml2-2.10.3-2-x86_64.pkg.tar.zst.sig
/var/cache/pacman/pkg/libxml2-2.10.3-2-x86_64.pkg.tar.zst
/var/cache/pacman/pkg/lib32-libxml2-2.10.3-2-x86_64.pkg.tar.zst
/var/cache/pacman/pkg/libxml2-2.10.3-2-x86_64.pkg.tar.zst.sig
/opt/calibre/lib/libxml2.so.2
find: ‘/run/user/1000/gvfs’: Permission denied
/usr/include/libxml2
/usr/include/libxml2/libxml
/usr/include/libxml2/libxml/xmlschemastypes.h
/usr/include/libxml2/libxml/SAX.h
/usr/include/libxml2/libxml/xmlschemas.h
/usr/include/libxml2/libxml/xmlreader.h
/usr/include/libxml2/libxml/c14n.h
/usr/include/libxml2/libxml/list.h
/usr/include/libxml2/libxml/uri.h
/usr/include/libxml2/libxml/nanohttp.h
/usr/include/libxml2/libxml/dict.h
/usr/include/libxml2/libxml/xlink.h
/usr/include/libxml2/libxml/xmlregexp.h
/usr/include/libxml2/libxml/xmlIO.h
/usr/include/libxml2/libxml/xmlversion.h
/usr/include/libxml2/libxml/xpointer.h
/usr/include/libxml2/libxml/schematron.h
/usr/include/libxml2/libxml/parserInternals.h
/usr/include/libxml2/libxml/xpathInternals.h
/usr/include/libxml2/libxml/xmlerror.h
/usr/include/libxml2/libxml/xmlunicode.h
/usr/include/libxml2/libxml/xmlautomata.h
/usr/include/libxml2/libxml/nanoftp.h
/usr/include/libxml2/libxml/HTMLtree.h
/usr/include/libxml2/libxml/debugXML.h
/usr/include/libxml2/libxml/threads.h
/usr/include/libxml2/libxml/pattern.h
/usr/include/libxml2/libxml/chvalid.h
/usr/include/libxml2/libxml/encoding.h
/usr/include/libxml2/libxml/xmlwriter.h
/usr/include/libxml2/libxml/globals.h
/usr/include/libxml2/libxml/HTMLparser.h
/usr/include/libxml2/libxml/entities.h
/usr/include/libxml2/libxml/parser.h
/usr/include/libxml2/libxml/tree.h
/usr/include/libxml2/libxml/xmlexports.h
/usr/include/libxml2/libxml/xmlstring.h
/usr/include/libxml2/libxml/catalog.h
/usr/include/libxml2/libxml/xmlmemory.h
/usr/include/libxml2/libxml/xmlmodule.h
/usr/include/libxml2/libxml/schemasInternals.h
/usr/include/libxml2/libxml/SAX2.h
/usr/include/libxml2/libxml/xpath.h
/usr/include/libxml2/libxml/xmlsave.h
/usr/include/libxml2/libxml/xinclude.h
/usr/include/libxml2/libxml/relaxng.h
/usr/include/libxml2/libxml/valid.h
/usr/include/libxml2/libxml/hash.h
/usr/lib/libxml2.so.2
/usr/lib/cmake/libxml2
/usr/lib/cmake/libxml2/libxml2-config.cmake
/usr/lib/libxml2.so
/usr/lib/girepository-1.0/libxml2-2.0.typelib
/usr/lib/python3.10/site-packages/libxml2mod.so
/usr/lib/python3.10/site-packages/drv_libxml2.py
/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.opt-1.pyc
/usr/lib/python3.10/site-packages/__pycache__/libxml2.cpython-310.pyc
/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.opt-1.pyc
/usr/lib/python3.10/site-packages/__pycache__/drv_libxml2.cpython-310.pyc
/usr/lib/python3.10/site-packages/libxml2.py
/usr/lib/libxml2.so.2.10.3
/usr/lib32/libxml2.so.2
/usr/lib32/cmake/libxml2
/usr/lib32/cmake/libxml2/libxml2-config.cmake
/usr/lib32/libxml2.so
/usr/lib32/libxml2.so.2.10.3
/usr/share/doc/xmlsec1/images/libxml2-logo.png
/usr/share/licenses/libxml2
/usr/share/licenses/libxml2/Copyright
/usr/share/licenses/lib32-libxml2
/usr/share/licenses/lib32-libxml2/Copyright

Actually, that’s to be expected. If you set timeshift to automatically take snapshots, it will keep copies of everything regularly.

I’m more concerned about the dependency issues your system is facing. When a package (calibre, in this case) runs fine on most systems but not on yours, it’s a sign of trouble.

Can you run this python -m pip list?

I want to see if you have accidentally installed python-lxml via pip. If you did, it would be prudent to compare its version to the one on the official repo.

Why python-lxml, you might ask? Well, python-lxml is the only package that tried to use a version of libxml2 that’s out of date.

Sorry I didn’t noticed your reply, here is the output:


❯ python -m pip list
Package            Version
------------------ -----------------
appdirs            1.4.4
argcomplete        2.0.0
attrs              22.1.0
autocommand        2.2.2
btrfsutil          6.0.2
cffi               1.15.1
chardet            5.0.0
colorama           0.4.6
cryptography       38.0.3
cssselect          1.2.0
Cython             0.29.32
defusedxml         0.7.1
docopt             0.6.2
future             0.18.2
Glances            3.3.0
greenlet           1.1.3.post0
inflect            6.0.2
jaraco.context     4.2.0
jaraco.functools   3.5.2
jaraco.text        3.11.0
lensfun            0.3.3
lxml               4.9.1
more-itertools     9.0.0
msgpack            1.0.4
nftables           0.1
numpy              1.23.5
nyx                2.1.0
onboard            1.4.1
ordered-set        4.1.0
packaging          21.3
Pillow             9.3.0
pip                22.3.1
ply                3.11
psutil             5.9.4
pyaml              21.10.1
pycairo            1.22.0
pycparser          2.21
pydantic           1.10.2
PyGObject          3.42.2
PyNaCl             1.4.0
pynvim             0.4.3
pyparsing          3.0.9
PyQt5              5.15.7
PyQt5-sip          12.11.0
python-xlib        0.32
PyYAML             6.0
readability        0.3.1
readability-lxml   0.8.1
Reflector          2021.11.20.2.41.3
setuptools         65.6.3
shadowsocks        3.0.0
shtab              1.5.8
six                1.16.0
stem               1.8.0
team               1.0
termcolor          2.1.0
tldr               3.1.0
toml               0.10.2
tomli              2.0.1
trash-cli          0.22.10.20
trove-classifiers  2022.10.19
typing_extensions  4.4.0
ueberzug           18.1.9
validate-pyproject 0.10.1
wheel              0.38.4
xmltodict          0.13.0
youtube-dl         2021.12.17
yq                 3.1.0

What I meant was that it is interesting that we can see the files even after uninstalled it. I installed timeshift very recently, it is a nice use of timeshift I had not think about.

I see that you have installed lxml using pip, and that version of lxml installed appears to match with the one in the official repo.

You might not think this is worth the trouble, but you could try to uninstall the version of lxml installed via pip and then install python-lxml from the official repo. After that, install calibre from the official repo again. It’s fine if you want to leave everything as it is; I’m just curious about why calibre doesn’t work on your system that’s all. If you do decide to try, make sure to check for dependencies—some other pip packages might depend on lxml.

Also, I see a lot of pip packages installed on your system that are all available on arch’s official repo.
pynvim, youtube-dl, etc. Did you install all these manually via pip?

It is not recommended for arch users to install global packages with package managers other than pacman/yay. If you must use pip, then it is best to create a virtual environment before doing so.

1 Like

I was wondering about why it is installed too.

I think I installed youtube-dl from pip as a habit from windows as I installed it like that, other than that I can’t remember installing them, maybe I installed it as a dependency for something else. I had no idea using pip can be replaced with pacman.

I want to reinstall calibre form arch repo but I want to make sure uninstalling lxml form pip is not going to break anything.

It is most likely installed as a dependency of other pip packages you installed.

I really don’t think that installing packages with third party package managers without the use of a virtual environment is a good idea. It will lead to problems eventually.

How I can do that? I am trying my best to stick to pacman too. But don’t know anything about virtual environment. Can you elaborate more on it?

To be honest, if I were in your position, I would do a clean reinstall and then set everything up from scratch, this time sticking to official repos/AUR only. If I have the time, I would not even hesitate. I personally can’t stand a messy system. :rofl:

Here’s a good article to help you understand virtual environments.

https://docs.python.org/3/library/venv.html

This post is also helpful if you are beginner. I posted it when I first started using arch-based distros.

I don’t like messy system too. I may do that in the future. but For now I think at least I need to learn more to know how to create a clean system and then migrate to that. I had tried Linux Mint on my old laptop just to learn these kinds of stuff, and it helped for sure, but I guess nothing can replace learning in action.

Thanks , learning anything related to this topics surely helps.