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Update

To eliminate most of the question in IRC (#pentoo) and to start a good documentation process, here are the steps to bring your system up to date.

WARNING: The errors on your screen need to be read and acted upon, following these directions blindly will result in failure, then ridicule, then more failure.

For the first time

Sync with the portage tree
emerge --sync
Modify /etc/portage/make.conf file for your system:

Please adjust your CFLAGS as desired, information can be found here: https://wiki.gentoo.org/wiki/CFLAGS Do not modify these FLAGS unless you know what you are doing, always check the defaults first with:

portageq envvar CFLAGS

This is the default for pentoo at the time of build:

# CFLAGS="-Os -mtune=nocona -pipe -ggdb"

A safe choice would be to keep whatever Pentoo defaults are, but optimize for your specific machine:

CFLAGS="${CFLAGS} -march=native"
CXXFLAGS="${CFLAGS}"
FCFLAGS="${CFLAGS}"
FFLAGS="${CFLAGS}"

MAKEOPTS is set automatically by the profile to jobs equal to processors, you do not need to set it.

ACCEPT_LICENSE="Oracle-BCLA-JavaSE NVIDIA-CUDA google-chrome Google-TOS PUEL baudline"

You may wish to edit your VIDEO_CARDS line to match your system better. Example, for nvidia/ati users should add nvdia/fglrx flags:

VIDEO_CARDS="fbdev vga vesa nvidia"

Guest OS users should add virtualbox/vmware or qxl flag(s):

VIDEO_CARDS="fbdev vga vesa virtualbox"
Modify your profile only if you know what you are doing, default should be fine for most users
eselect profile list
eselect profile set <number>

Follow the pentoo-updater below

On regular basis

Pay extra attention on upgrading kernel, gcc, python or any other system package. It is important to upgrade these packages properly before moving to the next step. You might also need to understand Upgrading Gentoo generic guideline.

Very recently some changes were pushed to Pentoo which moved the Pentoo Overlay from /var/lib/layman to /var/db/repos so:

If you have /var/db/repos/pentoo:
cd /var/db/repos/pentoo
git pull
./scripts/pentoo-updater.sh

everything should work now,

If you have /var/lib/layman/pentoo:
cd /var/lib/layman/pentoo
git pull
./scripts/pentoo-updater.sh

everything should work now,

This syncs the gentoo and pentoo repos like "apt-get update" in debian
emerge --sync
This updates all the normal packages like "apt-get upgrade" in debian
emerge --deep --update --newuse world -vt
This optionally merges in changed config files. unchanged files are merged automatically
etc-update
This removes old packages which are not needed like "apt-get autoremove" in debian
emerge --depclean
This rebuilds anything which may have been broken in update
emerge @preserved-rebuild
This checks all the programs installed from VCS for new revisions and updates if needed
smart-live-rebuild
Verifies there is no breakage after updates
revdep-rebuild
merge in any new config files
etc-update
clean up the distfiles/packages dirs to remove old/un-needed files
eclean-dist -d && eclean-pkg -d

Check /var/log/portage/elog/summary.log file

Kernel update

Follow the usual Gentoo way. Once the source is installed, download the latest config and run:

genkernel --no-clean --luks --gpg all
emerge @module-rebuild

and add a new boot menu in the /boot/grub/menu.lst file

You might need to run extra commands. For example:
emerge @x11-module-rebuild
eselect java-vm set system icedtea-bin-7

after python/perl upgrade:

perl-cleaner --modules
python-updater

Run the following command under each regular user's account

Regenerate the main menu for XFCE WM (or "-e" for e17, "-k" for KDE)
genmenu.py -x

Discussion and support available on irc.freenode.net #pentoo