default/linux/amd64/17.1 The amd64 17.1 profiles switch to a more standard 'no SYMLINK_LIB' multilib layout, and require an explicit migration. The migration is performed using the app-portage/unsymlink-lib tool. Read the Gentoo news item [2] for more information! The following steps can be used to upgrade your system: 1. Sync and upgrade your system to the newest package versions to reduce the risk of issues. 2. If you are still running a 13.0 profile, select gcc 6.4.0 or later as the system compiler, source /etc/profile and reinstall libtool: # gcc-config -l [1] x86_64-pc-linux-gnu-5.5.0 * [2] x86_64-pc-linux-gnu-8.3.0 # gcc-config 2 # . /etc/profile # emerge -1v libtool 3. Install the tool: # emerge -1v app-portage/unsymlink-lib 4. Run 'unsymlink-lib --analyze' and check the output for obvious mistakes. If you need to perform any changes to the system, remember to run 'unsymlink-lib --analyze' again afterwards. [past this point do not call emerge or modify /usr manually] 5. This is a very good time to make a backup. 6. Run 'unsymlink-lib --migrate'. You can add '--pretend' first to see what is going to happen. 7. Reboot your system. Check if important programs work. In particular, verify that e.g. 'emerge --info' works (but do not install anything). If you hit any serious problems, you can use 'unsymlink-lib --rollback' to revert the changes and return to step 3. 8. Run 'unsymlink-lib --finish'. You can add '--pretend' first to see what is going to happen but note that you're going to see a very long list of files to remove. 9. Switch the profile, e.g.: # eselect profile set default/linux/amd64/17.1/desktop [at this point you can start using emerge again. emerge will then not display this message anymore, but the remaining steps are still required!] 10. Rebuild the toolchain: # emerge -1v sys-devel/gcc:11 [ repeat for other slots you will be using ] [ if you are upgrading from 13.0 profile, also: ] # emerge -1v sys-devel/binutils # emerge -1v sys-libs/glibc 11. If you are using a multilib profile, rebuild all 32-bit packages. This can be done using: # emerge -1v --deep /lib32 /usr/lib32 /usr/lib/llvm/*/lib32 Alternatively, if you are switching from one of the 13.0 profiles you can rebuild all packages as detailed in the 17.0 news item: # emerge -ev @world 12. Once the last 32-bit package is rebuilt, your package manager should remove the orphaned /lib32 and /usr/lib32 symlinks. If that does not happen, remove them manually: # rm /lib32 /usr/lib32 For known issues, please see bug #506276 [1]. If you have any problems with the new profiles or the migration procedure, please report a bug and make it block the tracker. [1] bug #506276 [2] https://www.gentoo.org/support/news-items/2019-06-05-amd64-17-1-profiles-are-now-stable.html