epubcheck: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/epubcheck - from package: epubcheck

You may install the required package with command apt-get install {package}
Error in other languages:
epubcheck: bevel nie gevind nie
epubcheck: comandă negăsită
epubcheck: comando não encontrado
epubcheck: commande introuvable
epubcheck: command not found
epubcheck: käsku ei ole
epubcheck: không tìm thấy lệnh
epubcheck: komanda nerasta
epubcheck: Kommando nicht gefunden.
epubcheck: kommandot finns inte
epubcheck: komut yok
epubcheck: nie znaleziono polecenia
epubcheck: níor aimsíodh an t-ordú
epubcheck: no se encontró la orden
epubcheck: no s'ha trobat l'ordre
epubcheck: opdracht niet gevonden
epubcheck: parancs nem található
epubcheck: perintah tidak ditemukan
epubcheck: príkaz nenájdený
epubcheck: příkaz nenalezen
epubcheck: команда не найдена
epubcheck: командата не е открита
epubcheck: 命令找不到
epubcheck: コマンドが見つかりません