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I have an issue here:

I have a newly built Debian 9.2.1 System on Intel Atom. When I try to install Eclipse CDT (including all the dependencies) from the Synaptics package manager, it ejects the Debian Media and Synaptics gives the prompt to insert the Debian CD labeled ..... in /media/cdrom/

I am using a USB drive as my install media. I have tried three different ways to solve this out:

Insert the USB Device and mount it in /media/cdrom. Insert the Usb drive , let the system mount it default location and make a link to it from /media/cdrom/ Mount the ISO file for Debian Installation media to /media/cdrom The problem is that in every case it removes the CD ROM from /media/cdrom

and Synaptics keeps asking to insert the cdrom.

Does any body know how to resolve this ?

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I suspect you have this: http://novicenolonger.com/using-a-debian-iso-instead-of-a-cd-rom-in-your-sources-list/ setup. It is a link to setup a system to use the CD-ROM (media) instead of using the internet for updates. The system could be ejecting the media because it wants more media; which would contain the package it is looking for.

I would check: /etc/apt/sources.list which is your sources (mirror) list that tells your system where to find updates. Ensure your sources is pointed to a trusted debian repository and not to the media. Information from the debian wiki is here: https://wiki.debian.org/SourcesList.

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