apt doesn't seem to be working

Question

I've seen similar errors floating around but none of the fixes have seemed to work for me (I've tried removing all .disable files but get a 'no such file' in response)

I'm using Ubuntu 14.04 installed on a vendor supplied server I have admin privileges to. Any time I try to use apt-get install or apt-get upgrade etc. I get this output or similar and nothing seems to have changed or been installed:

admin@:$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
  authbind clusterssh gdebi-core genders ion-igv ion-jk libapache2-mod-jk
  libarchive13 libclass-data-inheritable-perl libcommons-collections3-java
  libcommons-dbcp-java libcommons-pool-java libdevel-stacktrace-perl
  libecj-java libelfg0 libexception-class-perl libgenders0
  libgeronimo-jta-1.1-spec-java libglib2.0-bin libhdb9-heimdal libkdc2-heimdal
  libnettle4 libntdb1 libpackagekit-glib2-16 libservlet3.0-java
  libtomcat7-java libtry-tiny-perl libx11-protocol-perl lsscsi packagekit
  packagekit-backend-aptcc packagekit-tools pdsh python-beautifulsoup
  python-calabash python-jsonpipe python-ntdb python3-chardet python3-debian
  python3-packagekit python3-pkg-resources python3-six tomcat7 tomcat7-admin
  tomcat7-common zeroinstall-injector
Use 'apt-get autoremove' to remove them.
The following packages have been kept back:
  isc-dhcp-client isc-dhcp-common libgl1-mesa-glx libglapi-mesa
  linux-headers-generic
0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
N: Ignoring file 'iontorrent-ubuntu.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'ionreporter-plugin.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'usb.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent-offcycle.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent-ubuntu.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'ionreporter-plugin.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'usb.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent-offcycle.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension

I'm not sure how or what I need to change to get just the standard Ubuntu 14.04 apt packages working.

I'm fairly new to this region of UNIX trouble shooting so any help would be fantastic! Please let me know if you need any additional info.

Edit 1: Per @Jos suggestion I call sudo apt update with similar result:

 Ign file: updates/ InRelease
Ign file: updates/ Release.gpg
Ign file: updates/ Release
Ign file: updates/ Translation-en_US
Ign file: updates/ Translation-en
Reading package lists... Done
N: Ignoring file 'iontorrent-ubuntu.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'ionreporter-plugin.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'usb.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent-offcycle.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
N: Ignoring file 'iontorrent.list.USBinstaller' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension

I believe this is because the vendor has the machine set to ignore the original apt manager configuration in favor of getting updates via their own personally hosted package files? I'm not sure how to either diagnose this or fix this issue.

Answer 1

Actually, nothing is really wrong here.

First, run sudo apt update to bring your packages database up to date with the repositories online.

You have a number of packages installed that are not used. They are just taking up space. Remove these with sudo apt autoremove.

You have a couple of updates that need a bit of attention. Those are "kept back" until you are certain that you want those to be installed. (It's usually safe to do so.). Install these with sudo apt dist-upgrade.

Remove the files called *.USBinstaller from the directory /etc/apt/sources.list.d. Use sudo from a command line to do so. I don't know where these come from, but I'm pretty sure you don't need them at this point. These files don't cause the apt process to fail though; as it says, they are simply ignored.