missing conf files noted on apt upgrade after distribution upgrade

[Eric Brown]

Since upgrading from 17.10 to 18.04, the following errors occur during routine apt upgrade:

/sbin/ldconfig.real: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf.d/i386-linux-gnu_EGL.conf: No such file or directory
/sbin/ldconfig.real: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf.d/i386-linux-gnu_GL.conf: No such file or directory

ProblemType: Bug
DistroRelease: Ubuntu 18.04
Package: ubuntu-release-upgrader-core 1:18.04.27
ProcVersionSignature: Ubuntu 4.15.0-38.41-generic 4.15.18
Uname: Linux 4.15.0-38-generic x86_64
NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
ApportVersion: 2.20.9-0ubuntu7.4
Architecture: amd64
CrashDB: ubuntu
CurrentDesktop: ubuntu:GNOME
Date: Tue Oct 30 16:26:01 2018
InstallationDate: Installed on 2018-03-07 (237 days ago)
InstallationMedia: Ubuntu 17.10 "Artful Aardvark" - Release amd64 (20180105.1)
PackageArchitecture: all
SourcePackage: ubuntu-release-upgrader
Symptom: release-upgrade
UpgradeStatus: Upgraded to bionic on 2018-08-02 (89 days ago)
VarLogDistupgradeTermlog:

[Eric Brown (eberic)]

The easy fix was to move the two links out of the /etc/ld.so.conf.d directory.

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[Jerzy Luszawski (dr-agon)]

The files /etc/ld.so.conf.d/i386-linux-gnu_EGL.conf and /etc/ld.so.conf.d/i386-linux-gnu_GL.conf are symlinks to /etc/alternatives/x86_64-linux-gnu_egl_conf /etc/alternatives/x86_64-linux-gnu_gl_conf, which are in turn the symlinks to /usr/lib/virtualbox/additions/00vboxvideo.conf (from VirtualBox package).

Update-initramfs seems to have problems with symlinks (why?).

Replacing the symbolic links with hard links (or just a copy of target file) resolves the warning, there is no need to remove the config files.
Note that updates or reinstallation of VirtualBox will break the link, so this is not a permanent solution.

[sr9000 (sr9000)]

Same symptoms like Jerzy Luszawski @dr-agon wrote, except my links pointing on:

/etc/ld.so.conf.d/i386-linux-gnu_GL.conf -> /etc/alternatives/i386-linux-gnu_gl_conf
/etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf -> /etc/alternatives/x86_64-linux-gnu_egl_conf
/etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf -> /etc/alternatives/x86_64-linux-gnu_gl_conf

alternatives are also symlinks, pointing to real files
/etc/alternatives/i386-linux-gnu_gl_conf -> /usr/lib/i386-linux-gnu/mesa/ld.so.conf
/etc/alternatives/x86_64-linux-gnu_egl_conf -> /usr/lib/x86_64-linux-gnu/mesa-egl/ld.so.conf
/etc/alternatives/x86_64-linux-gnu_gl_conf -> /usr/lib/x86_64-linux-gnu/mesa/ld.so.conf

When I copied real files into /etc/ld.so.conf.d/ the problem is gone.
`update-initramfs -u` didn't write any waning anymore.

Update-initramfs seems to have problems with symlinks (why?).

[Morten Frisch (fmfrisch)]

Upgraded from 16.04.5 to 18.04.3 and have noticed the same symptom

[Pri Vate (pri-v-ate)]

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