Could it be that, seven years later, I am having the same problem?

$ epubcheck -h > /tmp/log 2>&1
Gives an exit code 2 and here is the output of the log:
/usr/bin/epubcheck: ligne 1: $'PK\003\004' : commande introuvable
/usr/bin/epubcheck: ligne 8: erreur de syntaxe près du symbole inattendu « ( »
/usr/bin/epubcheck: ligne 8: `��&�'gs��g��ٚ���qPKمlT�D�E�
.5(META-INF/maven/org.w3c/epubcheck/pom.xml�ks�6���W������$;�5=�fkǏƩ7��nқ~?�J�]ڒ�#)��L����c��&���%
 ���ϷIL��T\�/6���
��PD<��������i��ѓa&�%5�T�ؘk��AB�Y�ӌ�s�9�ގ��-�b0wo��onn����lkk;�}|z
��Ti��V)���T�T��dF�aܪ�=���xc�d0LD���v�#35
0��I�g'�����0(0G��Sj�,���j8P����?��5e����@��K*�A=���&ltt����Ivw�{��h�\�������5S?��8K�"�h\���D�sFB��N��#���[�úE�<!�����OK,�ԼB��
    #2O     E�h͈�"Ef        p���������E�5��$�I���N`c��GhZ��q=�'>�
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$ file /usr/bin/epubcheck
/usr/bin/epubcheck: symbolic link to ../share/java/epubcheck.jar
$ file /usr/share/java/epubcheck.jar
/usr/share/java/epubcheck.jar: Zip archive data, at least v1.0 to
extract, compression method=store

It may be worth noting that this was working alright until recently.
Then I installed calibre, which I think did upgrade a number of
packages. Could it be that the kernel new how to execute Java files and
dooes no longer know  how to do that?

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