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I have a script that I merged into a single file by using pyinstaller. For the case, let´s do it with a simpler example, since the error also ocurrs:

helloworld.py

#!/bin/bash 
print "Hello World!"

By running pyinstaller --onefile helloworld.py, it creates the dist Folder with the executable file inside (helloworld).

I can run correctly this file on the terminal by typing ./helloworld, but it does not work if a make double-click, or right-click > Run.

Before you are asking, yes, in the properties of the file the Option Allow executing file as program is checked.

Also, in Nautilus, going to Edit > Preferences > Behavior, I already selected the option Ask each time for the Executable Text Files.

I am aware that there are many questions about the same thing, but I have tried everything and I couldn´t solve the problem still. Does anyone know what can be happening? Thanks in advance.

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In fact the file is executed, but running a program from Nautilus doesn't open it in a terminal. The best way to run a software is create a shell desktop entry within /usr/share/applications or ~/.local/share/applications. Desktop with be named something like helloworld.desktop and should contain the following example:

[Desktop Entry]

# The type as listed above
Type=Application

# The version of the desktop entry specification to which this file complies
Version=1.0

# The name of the application
Name=HelloWorld

# A comment which can/will be used as a tooltip
Comment=This is just a sample

# The path to the folder in which the executable is run
Path=/opt/helloworld/

# The executable of the application, possibly with arguments.
Exec=/opt/helloworld/helloworld

# The name of the icon that will be used to display this entry
Icon=/path/to/an/icon.svg

# Describes whether this application needs to be run in a terminal or not
Terminal=true

# Describes the categories in which this entry should be shown
Categories=Misc;Languages;Python;

Source of the information : https://wiki.archlinux.org/index.php/desktop_entries

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