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LIsLinuxIsSogood
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PostPosted: Sun Feb 14, 2016 2:11 am    Post subject: I had a nice system, until...kernel uninstall due to & Reply with quote

[topic=]I wanted a window manager like X and now have zilch

I am new to the forum so thanks to that I may not be doing exactly whatever it is I've seen.

To start, I had a bootable system as recent as two or three days ago, when while working within a fairly minimal installation I did of the system with Gentoo kernel sources (4.1.12-gentoo at the time). So far, you may be thinking why is this posted under desktop env instead of kernel, I am of course eager to explain. The course of action that led to the kernel panic (and the non bootable system???) is likely to have been stemmed from my attempts to install an X server on it. Of course if that's not believable the real reason is my own questionable attempt at removing incorrect packages that were supposed to be part of the windows manager/server.

I think what did it was the a -–depclean option and since that the absence of files in the source directory of the initial, including, Kconfig and several other important files like the Makefile under source 4.1.12 What does that mean? If those files exist elsewhere then because I now have the sources for three different kernels merged under /usr/src/ directory and no apparent objective in mind.

Most of my effort has been to install a patched version of the kernel I was never supposed to be on my sustem.

e the patch kernel is 4.1.15 – Gentoo– R1 and if I had correct instructions for the X11 installation that led me to here. Iam certainly not going to be using any features of the portage system without prior knowledge.
To be honest although I am fairly certain of it, The problem could be something other than a panic!

The missing files, the panic message at boot time when screen locks, and the absence of listing of profile selection for kernel using eselect.

I'm a newbie could someone point me Towards a productive means of searching for the answers within logs, messages or forum. Thank you!
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ct85711
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PostPosted: Sun Feb 14, 2016 2:50 am    Post subject: Reply with quote

Ok, first off it would be better I explain about the kernel packages. When ever portage downloads a kernel, unlike other packages, it does not compile it in anyway; only installs the source files in /usr/src. You have to manually go into the kernel's directory and configure, compile, and install the built kernel. When you install the kernel, it copies all of the compiled modules, and install them onto your system (iirc, somewhere like /usr/lib/ area) and usualy it will copy the compiled kernel image to your /boot (vmlinuz, it may not copy the kernel over there). You have to be sure you have the boot partition mounted prior (frequently a common issue). Note: You also have to update your boot loader's configuration to let it know of the new kernel image, it does not do it automatically)

Now when you have portage remove a kernel, it will only remove any uncompiled/modified files; the compiled parts are left there in the directory. You have to remove the rest of the kernel files yourself.
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LIsLinuxIsSogood
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PostPosted: Sun Feb 14, 2016 6:33 am    Post subject: Reply with quote

Thank you ct I was thinking about the portage trees as well, but now I believe it could be a focal point even... you mentioned kernel removal, something that I am not sure how it happened even. What else regarding portage or even Filesystem management would result in the disappearance of just the key components to the kernel's build???

As for the compiled kernel from before; it seems odd (unless it is a result of running a thorough "removal") that I can't find the image anywhere on my drive for the kernel which was working fine until recently. Also, since there is no way to restore for me (ouch) I would like to ask about suppose you might explain a way of using emerge to find the source again. That is for the earlier release (4.1.12)...please?
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Xywa
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PostPosted: Sun Feb 14, 2016 6:56 am    Post subject: Reply with quote

Could you put:
Code:
$ uname -a

and
Code:
$ emerge --info

and
Code:
$ emerge -s gentoo-source
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LIsLinuxIsSogood
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PostPosted: Sun Feb 14, 2016 9:15 am    Post subject: Reply with quote

Quote:
4.1.12-gentoo

Thanks by the way for the quick reply, and
For the #2 emerge and emerge --info


Quote:
[ Results for search key : gentoo-source ]
Searching...

* sys-kernel/gentoo-sources
Latest version available: 4.1.15-r1
Latest version installed: 4.1.15-r1
Size of files: 81,531 KiB
Homepage: https://dev.gentoo.org/~mpagano/genpatches
Description: Full sources including the Gentoo patchset for the 4.1 kernel tree
License: GPL-2 freedist

[ Applications found : 1 ]



Here's the one in the middle
Quote:
Keep in mind I am sort of looking for a magic bullet like a totally cool way of restoring (yet without having previously backed up!!!!!!!)...I know that's not how it works, but if it doesn't suggest a clean install I'm open to anything. Really, I just want to get the thing up so I can then backup the entire system onto a couple DVDs or something.


Portage 2.2.26 (python 3.4.3-final-0, default/linux/amd64/13.0/no-multilib, gcc-4.9.3, glibc-2.21-r1, 4.1.12-gentoo x86_64)
=================================================================
System uname: Linux-4.1.12-gentoo-x86_64-Intel-R-_Pentium-R-_CPU_G2120_@_3.10GHz-with-gentoo-2.2
KiB Mem: 8129452 total, 5299740 free
KiB Swap: 0 total, 0 free
Timestamp of repository gentoo: Sun, 24 Jan 2016 04:00:01 +0000
sh bash 4.3_p42-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash: 4.3_p42-r1::gentoo
dev-lang/perl: 5.20.2::gentoo
dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/pkgconfig: 0.28-r2::gentoo
sys-apps/baselayout: 2.2::gentoo
sys-apps/openrc: 0.19.1::gentoo
sys-apps/sandbox: 2.10-r1::gentoo
sys-devel/autoconf: 2.69::gentoo
sys-devel/automake: 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils: 2.25.1-r1::gentoo
sys-devel/gcc: 4.9.3::gentoo
sys-devel/gcc-config: 1.7.3::gentoo
sys-devel/libtool: 2.4.6::gentoo
sys-devel/make: 4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc: 2.21-r1::gentoo
Repositories:

gentoo
location: /usr/portage
sync-type: rsync
sync-uri: rsync://rsync.gentoo.org/gentoo-portage
priority: -1000

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx mmxext modules ncurses netifrc nls nptl openmp pam pcre readline seccomp session sse sse2 ssl tcpd unicode xattr zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
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NeddySeagoon
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PostPosted: Sun Feb 14, 2016 9:55 am    Post subject: Reply with quote

LIsLinuxIsSogood,

Welcome to Gentoo
emerging a kernel is special. Unlike other packages, it only installs the sources into /usr/src
The rest is up to you. Conversely, only the sources are removed by portage when you clean up.

Since your system used to boot but doesn't now, only a small number of things can have happened.
a) your boot loader configuration is messed up.
b) your initrd is missing
c) you changed your good kernel for a broken kernel trying to get Xorg to work.

We know you were trying to get Xorg to work, so you have probably made some accidental changes to your kernel.

Please tell how you made your working kernel.
If you repeat those steps, it should work again.

The lesson from this is to not overwrite your working kernel with one you are testing.
Everyone builds a dud kernel now and again. Its good to pick another kernel from the boot menu to recover.
_________________
Regards,

NeddySeagoon

Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail.
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Xywa
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PostPosted: Sun Feb 14, 2016 11:47 am    Post subject: Reply with quote

LIsLinuxIsSogood wrote:


Quote:
4.1.12-gentoo

Code:
*  sys-kernel/gentoo-sources
      Latest version available: 4.1.15-r1
      Latest version installed: 4.1.15-r1


^^ Some kind of mismatch?

Maybe your problem is related to last xorg-server and nvidia optimus? What graphic card do you use?
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spikyatlinux
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PostPosted: Sun Feb 14, 2016 9:15 pm    Post subject: Reply with quote

After updating your kernel its good to rebuild the modules with the following command

Code:
emerge --ask --verbose @module-rebuild


The procedure of an kernel update is always the same, I use:

Code:

emerge -u gentoo-sources or emerge -vuDN @world


cd in /usr/src

Code:
eselect kernel list

Code:
eselect kernel set 1
or whatever looks like your new version perhaps 2 or 3 depending on how many kernels are installed.

copy old and running kernel config to the new sources dir. Example

Code:
cp -v /usr/src/linux-4.1.12-gentoo/.config /usr/src/linux-4.1.15-gentoo-r1


cd in new kernel directory

You are in /usr/src after selecting the right kernel with eselect build as follows

Code:

cd linux
make oldconfig
make -j$(nproc)
make modules_install
make install


rebuild modules
Code:
emerge --ask --verbose @module-rebuild


this is neccessary for nvidia to work and perhaps

Code:
emerge --ask --verbose x11-module-rebuild


Finally update your grub config

Code:
grub-mkconfig -o /boot/grub/grub.cfg


And your done, best of luck


Last edited by spikyatlinux on Mon Feb 15, 2016 8:31 am; edited 1 time in total
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 1:00 am    Post subject: Reply with quote

Xywa wrote:


Maybe your problem is related to last xorg-server and nvidia optimus? What graphic card do you use?


I thought this too, but it probably is jus t coincidental because of the incorrect packages associated with X. The Card is a GTX 660 and What I can't seem to figure out is if the firmware requires some Nvidia drivers or if I should be able to use open-source, preferably...nouveau.

Also, in terms of the system, it would appear something has changed and while I have yet to attempt to logout of the chroot environment I now have the three kernel packages available to me and can use the "set" feature too for kernel eselect. Is there any way of predicting if the problem will occur with the older vs the newer kernel should I select either one of those? The third option is not configured yet, so I've ruled it out, but that one is 4.3.3-hardened-r4.

My own feeling tells me to go back to the first kernel - the only one that ever properly was able to boot, and then to follow instrutions of fellow n00b to spikyatlinux to rebuild modules after an update to the kernel?
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 1:17 am    Post subject: Reply with quote

Could someone maybe also tell me why I might need an initramfs for the particular NVidia card, or if I choose to build the latest kernel will it work without the ramdisk for boot. I'm trying to figure out which of the many files in my /boot directory can be removed, and if so maybe there is a better way than just using rm to remove those files, is there?
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spikyatlinux
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PostPosted: Mon Feb 15, 2016 6:26 am    Post subject: Reply with quote

Whats does the command
Code:
eselect opengl list
shows?
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 6:42 am    Post subject: Reply with quote

It lists xorg-x11

I think something is wrong with the bootloader too...I get a long string of errors perhaps there is a file that needs updating before GRUB2 will allow it, or else maybe I will attempt a non grub boot using some other mode of operations on the filesystem...any thoughts? Would it make more sense perhaps to reinstall grub and then try it out on the newer kernel, hopefully with the OpenGL library for now?
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 7:22 am    Post subject: Reply with quote

Well, I was able to manually configure the bootloader which was the cause of some immediate problem with booting, since I am now logged in with a single user but not very stable system.

For example, the device block partition for the boot sector is missing mmost of the normal files that ordinarily reside in the /boot folder, and those that are there do not correspond to the current state of the system, in terms of the kernel structure and why that is I don't know...I am not even certain other than the changes I made, what else may have caused me to be able to find a work around of the problem but it has at least given me some way around that.

Through the couple minor adjustments to one of the entries (of the grub.cfg file) including removal of a line for initrd. that I thought might be conflicting with the Filesystem.

Now I will try another entry and eventually need to clean up the number of unneccesary entries in the bootloader. This is beginning to appear as Mr. long time ago mentioned about 1 2 and 3 possible remedies to the situation. And hopefully, more of the files in boot partition will be visible later as well. Thank you all for your concern.

I learned some real good stuff right now about the operability of a system that has yet to really properly implement the use of a graphics card although the software is clearly on there. It is cool! Thanks to all!
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spikyatlinux
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PostPosted: Mon Feb 15, 2016 7:37 am    Post subject: Reply with quote

Normally the output should look like
Code:
eselect opengl list
Available OpenGL implementations:
  [1]   nvidia *
  [2]   xorg-x11


Create a copy of your boot directory and copy kernel related files to with the following commands
As I know there are some problems with hardened gentoo sources+nvidia use normal gentoo-sources.

cd in /usr/src select latest booting kernel with
Code:
eselect kernel set [NUMBER OF BOOTING KERNEL]


Code:
cp -a /boot /boot.bck
rm -rf /boot/*


Quote:
cd linux
make install <<<---- Then there should be the kernel files (vmlinuz-4.1.15-gentoo-r1,System.map-4.1.15-gentoo-r1 and config-4.1.15-gentoo-r1) in your boot directory


Code:
rm -rf /lib/modules/*
make modules_install <<<---- To reinstall the previous deleted files


Code:
emerge --ask --verbose @module-rebuild or emerge --ask --verbose --oneshot x11-drivers/nvidia-drivers


Code:
grub-install /dev/sdA <<<---- Reinstall grub on your boot partition ATTENTION to use the right partition !!!
grub-mkconfig -o /boot/grub/grub.cfg


Code:
eselect opengl set nvidia


You should see something like Switching to nvidia OpenGL interface... done

Remove /etc/X11/xorg.conf if it exists and create new one with

Code:
nvidia-xconfig


Create new one

Check all commands I´m not responsible for anything ;-)
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spikyatlinux
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PostPosted: Mon Feb 15, 2016 7:41 am    Post subject: Reply with quote

Go to http://kmuto.jp/debian/hcl/ on your console type
Code:
lspci -n
copy the output to that page. You will see your needed kernel modules. Beware that kernel names use underline _ and not -.
If you compiled the needed modules in your kernel you don´t need an initrd. I´ve never using an initrd file, on my gentoo box.

Regards
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spikyatlinux
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PostPosted: Mon Feb 15, 2016 8:06 am    Post subject: Reply with quote

You can´t get it run you have falsed to set nvidia in your make.conf please add
Code:
VIDEO_CARDS="nvidia"
in your
Code:
/etc/portage/make.conf
be aware that this set only once. Then run
Code:
emerge -avuDN @world
there should be some rebuilds of xorg and nvidia, after that you should be able to set nvidia with eselect.
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 8:09 am    Post subject: Reply with quote

Thanks for the tip...but it unfortunately didn't work to provide any more information about the drivers or kernel associated with my particular card (fyi)... there is a column for Works- what does that column propose to explain exactly? Why is the NVidia driver the better option for this card (GeForce GTX 660)
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 8:16 am    Post subject: Reply with quote

Hey spikyatlinux what does the --oneshot option with x11-drivers effectively propose to do? Because, so far I have not gotten emerge to recognize that package for the drivers yet.

spikyatlinux wrote:
Normally the output should look like
Code:
eselect opengl list
Available OpenGL implementations:
  [1]   nvidia *
  [2]   xorg-x11


Create a copy of your boot directory and copy kernel related files to with the following commands
As I know there are some problems with hardened gentoo sources+nvidia use normal gentoo-sources.

cd in /usr/src select latest booting kernel with
Code:
eselect kernel set [NUMBER OF BOOTING KERNEL]


Code:
cp -a /boot /boot.bck
rm -rf /boot/*


Quote:
cd linux
make install <<<---- Then there should be the kernel files (vmlinuz-4.1.15-gentoo-r1,System.map-4.1.15-gentoo-r1 and config-4.1.15-gentoo-r1) in your boot directory


Code:
rm -rf /lib/modules/*
make modules_install <<<---- To reinstall the previous deleted files


Code:
emerge --ask --verbose @module-rebuild or emerge --ask --verbose --oneshot x11-drivers/nvidia-drivers


Code:
grub-install /dev/sdA <<<---- Reinstall grub on your boot partition ATTENTION to use the right partition !!!
grub-mkconfig -o /boot/grub/grub.cfg


Code:
eselect opengl set nvidia


You should see something like Switching to nvidia OpenGL interface... done

Remove /etc/X11/xorg.conf if it exists and create new one with

Code:
nvidia-xconfig


Create new one

Check all commands I´m not responsible for anything ;-)
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LIsLinuxIsSogood
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PostPosted: Mon Feb 15, 2016 8:22 am    Post subject: Reply with quote

USE flags perhaps...are they part of the rebuild? If not, I think I will go back to the handbook after this one. Since I may just want to get more comfortable with installing and removing packages before I go to a Graphical user interface. Thanks again Spiky at Linux...
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spikyatlinux
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PostPosted: Mon Feb 15, 2016 8:29 am    Post subject: Reply with quote

--oneshot (-1)
Emerge as normal, but do not add the packages to the world file for later updating.

WARNING: This option should only be used for packages that are reachable from the @world package set (those that would not be removed by --depclean),
since dependencies of unreachable packages are allowed to be broken when satisfying dependencies of other packages. Broken dependencies of this sort
will invalidate assumptions that make it possible for --deep to be disabled by default.
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spikyatlinux
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PostPosted: Mon Feb 15, 2016 8:38 am    Post subject: Reply with quote

LIsLinuxIsSogood wrote:
Thanks for the tip...but it unfortunately didn't work to provide any more information about the drivers or kernel associated with my particular card (fyi)... there is a column for Works- what does that column propose to explain exactly? Why is the NVidia driver the better option for this card (GeForce GTX 660)


The nvidia proprietary driver includes native support for your card. There is a nice article you can read http://www.pcworld.com/article/2911459/why-nvidia-graphics-cards-are-the-worst-for-open-source-but-the-best-for-linux-gaming.html
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LIsLinuxIsSogood
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PostPosted: Tue Jan 17, 2017 7:43 am    Post subject: Reply with quote

8O
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Roman_Gruber
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PostPosted: Tue Jan 17, 2017 9:24 pm    Post subject: Reply with quote

Did you read the gentoo wiki about nvidia-driver setup?

I have a 660m gtx and the gentoo wiki is still a good starting point.

the binary driver usually works. the open source one may work with older cards.

just for your information

nvidia => binary nvidia-driver package
noveau => open source drivers. check that project homepage what is supported. my card is not that well supported, last time i have checked.

both need different settings in make.conf and kernel.

Quote:
USE flags perhaps...are they part of the rebuild? If not, I think I will go back to the handbook after this one. Since I may just want to get more comfortable with installing and removing packages before I go to a Graphical user interface. Thanks again Spiky at Linux...


Use flags is the term for all those customizations you can choose for those packages.
ufed is an editor where you can see the most common use-flags explained. you can also set them there.

https://wiki.gentoo.org/wiki/USE_flag
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LIsLinuxIsSogood
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PostPosted: Tue Jan 17, 2017 9:51 pm    Post subject: Reply with quote

Yes, and that's been a good resource, the configuration however is another story, by the way! I'm sure something was in there that mentions it but i'll have to double check now, what really made a difference on the latest install of proprietary nvidia drivers (in addition to the help provided in this forum) was to reinstall Xorg server afterwards. Note: K haven't had to do this again yet, but there is a recommendation to each time upgrading the kernel reinstalling the drivers. Thanks for the help soon I'll be installing my first virtual system and will likely need to have some repeated success with the information provided in these sources, the forum and the wiki. Thanks
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NeddySeagoon
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PostPosted: Tue Jan 17, 2017 11:37 pm    Post subject: Reply with quote

LIsLinuxIsSogood,

Each time you upgrade the kernel you must rebuild any out of kernel modules against the new kernel
The nVidia kernel module is one such example.
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Regards,

NeddySeagoon

Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail.
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