I believe I also have this issue. I see the issue each time I run "apt upgrade".
The symlink chain goes to a real file. If you cat the contents of the symlink you do see the file's ascii contents, which is a directory. That directory also exists, and has files. I'm not sure if it is related but my /boot directory is full of old kernels that keep being regenerated. These kernels are not installed according to package management. # apt upgrade ... update-initramfs: Generating /boot/initrd.img-4.13.0-43-generic /sbin/ldconfig.real: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf: No such file or directory ls -la /etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf lrwxrwxrwx 1 root root 43 Sep 26 2014 /etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf -> /etc/alternatives/x86_64-linux-gnu_egl_conf # cat /etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf /usr/lib/x86_64-linux-gnu/libhybris-egl # ls -la /usr/lib/x86_64-linux-gnu/libhybris-egl total 288 drwxr-xr-x 2 root root 4096 Oct 22 2017 . drwxr-xr-x 142 root root 135168 Feb 6 14:07 .. -rw-r--r-- 1 root root 1 Sep 20 2017 alt_ld.so.conf -rw-r--r-- 1 root root 40 Sep 20 2017 ld.so.conf lrwxrwxrwx 1 root root 15 Sep 20 2017 libEGL.so.1 -> libEGL.so.1.0.0 -rw-r--r-- 1 root root 22648 Sep 20 2017 libEGL.so.1.0.0 lrwxrwxrwx 1 root root 21 Sep 20 2017 libGLESv1_CM.so.1 -> libGLESv1_CM.so.1.0.1 -rw-r--r-- 1 root root 79824 Sep 20 2017 libGLESv1_CM.so.1.0.1 lrwxrwxrwx 1 root root 18 Sep 20 2017 libGLESv2.so.2 -> libGLESv2.so.2.0.0 -rw-r--r-- 1 root root 26592 Sep 20 2017 libGLESv2.so.2.0.0 lrwxrwxrwx 1 root root 23 Sep 20 2017 libwayland-egl.so.1 -> libwayland-egl.so.1.0.0 -rw-r--r-- 1 root root 6024 Sep 20 2017 libwayland-egl.so.1.0.0 # uname -a Linux mgmt1 4.13.0-43-generic #48-Ubuntu SMP Wed May 16 12:18:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1800719 Title: missing conf files noted on apt upgrade after distribution upgrade To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ubuntu-release-upgrader/+bug/1800719/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
