[gentoo-user] /usr/src/linux gone

[gentoo-user] /usr/src/linux gone

[sean]

I just did an update of my system and now the linux directory under
/usr/src is not there.
In fact under /usr/src there is nothing.

Something change or would anyone have any ideas of what might have
happened, and how to fix?

			Thanks
			Sean

Re: [gentoo-user] /usr/src/linux gone

[Alan McKinnon]

On 10/03/11 01:29, sean wrote:
> I just did an update of my system and now the linux directory under
> /usr/src is not there.
> In fact under /usr/src there is nothing.
> 
> Something change or would anyone have any ideas of what might have
> happened, and how to fix?

You rm'ed it while doing a fantastic imitation of a numbnut?
Portage for sure did not do it, so that leaves you.

emerge <kernel of your choice>
cd /usr/src
ln -s <kernel of your choice> linux
cd linux
zcat /proc/config.gz > .config
make oldconfig
make menuconfig
make

There's a USE flag that makes this a tad less manual, but you get the idea.

-- 
alan dot mckinnon at gmail dot com

Re: [gentoo-user] /usr/src/linux gone

[sean]

On 03/09/2011 06:41 PM, Alan McKinnon wrote:

> 
> You rm'ed it while doing a fantastic imitation of a numbnut?
> Portage for sure did not do it, so that leaves you.

I did not delete it.

Re: [gentoo-user] /usr/src/linux gone

[Alan McKinnon]

On 10/03/11 01:51, sean wrote:
> On 03/09/2011 06:41 PM, Alan McKinnon wrote:
> 
>>
>> You rm'ed it while doing a fantastic imitation of a numbnut?
>> Portage for sure did not do it, so that leaves you.
> 
> I did not delete it.


Well I don't know where your files went.

But I described how to put them back

-- 
alan dot mckinnon at gmail dot com

Re: [gentoo-user] /usr/src/linux gone

[Dale]

sean wrote:
> On 03/09/2011 06:41 PM, Alan McKinnon wrote:
>
>    
>> You rm'ed it while doing a fantastic imitation of a numbnut?
>> Portage for sure did not do it, so that leaves you.
>>      
> I did not delete it.
>
>
>    

Did you perhaps run --depclean and it removed it?  That's the only way I 
can think of that emerge would remove it.  Otherwise, it was you.  O_O

Dale

:-)

Re: [gentoo-user] /usr/src/linux gone

[Peter Humphrey]

On Thursday 10 March 2011 03:31:55 Dale wrote:

> Did you perhaps run --depclean and it removed it?  That's the only way I
> can think of that emerge would remove it.

Depclean might have removed the files from the source package, but it 
wouldn't have removed .config or anything resulting from compilation. Not 
unless it's horribly broken, in which case I'm sure we'd have heard by now.

-- 
Rgds
Peter

Re: [gentoo-user] /usr/src/linux gone

[Jesús J. Guerrero Botella]

As someone said above, a possible cause is that /usr/src was a mount
point, maybe with -obind, or even a symlink. Many people do this to
handle kernels manually on their own $HOME directory (I do it this way
myself).

Another random cause I can think of would be some of the cruft
cleaning scripts that there are around and that are not part of
Gentoo.

On a more paranoid though, it could also be a rootkit, or maybe your
box was hacked.

But, otherwise, you removed it, maybe without noticing.

--depclean would never remove this, even if it was buggy enough to
remove all your kernels (which it isn't) it wouldn't remove all the
files that do not belong to the package, and there are thousands of
these in any kernel tree that's been configured and/or compiled.
Hence, the non-empty directories would never be removed either.

-- 
Jesús Guerrero Botella

Re: [gentoo-user] /usr/src/linux gone

[sean]

On Mar 10, 2011, at 6:30 AM, Jesús J. Guerrero Botella wrote:
> 
> 
> Another random cause I can think of would be some of the cruft
> cleaning scripts that there are around and that are not part of
> Gentoo.
> 
> On a more paranoid though, it could also be a rootkit, or maybe your
> box was hacked.
> 
> But, otherwise, you removed it, maybe without noticing.
> 
> --depclean would never remove this, even if it was buggy enough to
> remove all your kernels (which it isn't) it wouldn't remove all the
> files that do not belong to the package, and there are thousands of
> these in any kernel tree that's been configured and/or compiled.
> Hence, the non-empty directories would never be removed either.
> 
> -- 
> Jesús Guerrero Botella
> 
> 

If you have anything you wish me to check, I will.
But I know that I did not remove it.

I su'd in the terminal, started the updates, and as mentioned eventually saw the nvidia-drivers complaining about not finding a .config.
That is what led me to discover the missing directory.
I update the system regularly.

Re: [gentoo-user] /usr/src/linux gone

[Gregory Fontenele]

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way out of this list?

On Sat, Mar 12, 2011 at 09:11, sean <tech.junk@myfairpoint.net> wrote:

>
> On Mar 10, 2011, at 6:30 AM, Jesús J. Guerrero Botella wrote:
> >
> >
> > Another random cause I can think of would be some of the cruft
> > cleaning scripts that there are around and that are not part of
> > Gentoo.
> >
> > On a more paranoid though, it could also be a rootkit, or maybe your
> > box was hacked.
> >
> > But, otherwise, you removed it, maybe without noticing.
> >
> > --depclean would never remove this, even if it was buggy enough to
> > remove all your kernels (which it isn't) it wouldn't remove all the
> > files that do not belong to the package, and there are thousands of
> > these in any kernel tree that's been configured and/or compiled.
> > Hence, the non-empty directories would never be removed either.
> >
> > --
> > Jesús Guerrero Botella
> >
> >
>
> If you have anything you wish me to check, I will.
> But I know that I did not remove it.
>
> I su'd in the terminal, started the updates, and as mentioned eventually
> saw the nvidia-drivers complaining about not finding a .config.
> That is what led me to discover the missing directory.
> I update the system regularly.
>



-- 
Atenciosamente,
Gregory Fontenele

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Re: [gentoo-user] /usr/src/linux gone

[Arttu V.]

On 3/12/11, sean <tech.junk@myfairpoint.net> wrote:
> If you have anything you wish me to check, I will.

It's probably too late to think about this option, but just in case:
you don't happen to have a copy of root's bash history from around the
time you noticed the problem?

-- 
Arttu V.

Re: [gentoo-user] /usr/src/linux gone

[Thanasis]

on 03/12/2011 02:11 PM sean wrote the following:
> I su'd in the terminal, started the updates, and as mentioned
> eventually saw the nvidia-drivers complaining about not finding a .config.
Not finding a .config is an indication that the kernel source may have
never been touched (configured) so all files (including the directory)
might be removed by an emerge --depclean.
> That is what led me to discover the missing directory.
> I update the system regularly.

Re: [gentoo-user] /usr/src/linux gone

[Matthew Finkel]

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2011/3/12 Thanasis <thanasis@asyr.hopto.org>

> on 03/12/2011 02:11 PM sean wrote the following:
> > I su'd in the terminal, started the updates, and as mentioned
> > eventually saw the nvidia-drivers complaining about not finding a
> .config.
> Not finding a .config is an indication that the kernel source may have
> never been touched (configured) so all files (including the directory)
> might be removed by an emerge --depclean.
> > That is what led me to discover the missing directory.
> > I update the system regularly.
>
> But if this was a pre-existing build, he should have had numerous kernels
configured, unless he removed/moved the config each time he upgraded.

Sean,

Two questions. I don't think you ever replied as to whether /usr/src is a
mounted partition, is it? Also, did you have multiple kernels emerged into
different slots before this happened? if so, does portage still think
they're installed?

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Re: [gentoo-user] /usr/src/linux gone

[sean]

On 03/12/2011 01:28 PM, Matthew Finkel wrote:

> 
> But if this was a pre-existing build, he should have had numerous
> kernels configured, unless he removed/moved the config each time he
> upgraded. 
> 
> Sean,
> 
> Two questions. I don't think you ever replied as to whether /usr/src is
> a mounted partition, is it? Also, did you have multiple kernels emerged
> into different slots before this happened? if so, does portage still
> think they're installed?

It was not a mounted partition.
No multiple kernels. I try to clean up after myself.

Re: [gentoo-user] /usr/src/linux gone

[Matthew Finkel]

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On Sun, Mar 13, 2011 at 8:46 AM, sean <tech.junk@myfairpoint.net> wrote:

> On 03/12/2011 01:28 PM, Matthew Finkel wrote:
>
> >
> > But if this was a pre-existing build, he should have had numerous
> > kernels configured, unless he removed/moved the config each time he
> > upgraded.
> >
> > Sean,
> >
> > Two questions. I don't think you ever replied as to whether /usr/src is
> > a mounted partition, is it? Also, did you have multiple kernels emerged
> > into different slots before this happened? if so, does portage still
> > think they're installed?
>
> It was not a mounted partition.
> No multiple kernels. I try to clean up after myself.
>
>
Is it possible you ran depclean prior to compiling the newest kernel that
you emerged?

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Re: [gentoo-user] /usr/src/linux gone

[Matthew Finkel]

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On Tue, Mar 15, 2011 at 10:13 AM, Matthew Finkel
<Matthew.finkel@gmail.com>wrote:

>
>
> On Sun, Mar 13, 2011 at 8:46 AM, sean <tech.junk@myfairpoint.net> wrote:
>
>> On 03/12/2011 01:28 PM, Matthew Finkel wrote:
>>
>> >
>> > But if this was a pre-existing build, he should have had numerous
>> > kernels configured, unless he removed/moved the config each time he
>> > upgraded.
>> >
>> > Sean,
>> >
>> > Two questions. I don't think you ever replied as to whether /usr/src is
>> > a mounted partition, is it? Also, did you have multiple kernels emerged
>> > into different slots before this happened? if so, does portage still
>> > think they're installed?
>>
>> It was not a mounted partition.
>> No multiple kernels. I try to clean up after myself.
>>
>>
> Is it possible you ran depclean prior to compiling the newest kernel that
> you emerged?
>
Actually, scratch that though. Do you have any emerged packages that depend
directly on gentoo-sources?

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Re: [gentoo-user] /usr/src/linux gone

[sean]

On Mar 15, 2011, at 10:13 AM, Matthew Finkel wrote:
> 
> 
> Is it possible you ran depclean prior to compiling the newest kernel that you emerged? 

Do not think so.
I keep things up to date and there were no warnings flags such as the nvidia-drivers that notified me of the missing .config in usr/src/linux.

Re: [gentoo-user] /usr/src/linux gone

[sean]

On Mar 10, 2011, at 5:12 AM, Peter Humphrey wrote:

> On Thursday 10 March 2011 03:31:55 Dale wrote:
> 
>> Did you perhaps run --depclean and it removed it?  That's the only way I
>> can think of that emerge would remove it.
> 
> Depclean might have removed the files from the source package, but it 
> wouldn't have removed .config or anything resulting from compilation. Not 
> unless it's horribly broken, in which case I'm sure we'd have heard by now.
> 
> -- 
> Rgds
> Peter
> 

I do run depclean after updating the system.
Still at a loss as to the cause.

[gentoo-user] Re: /usr/src/linux gone

[walt]

On 03/09/2011 03:29 PM, sean wrote:
> I just did an update of my system and now the linux directory under
> /usr/src is not there.
> In fact under /usr/src there is nothing.
>
> Something change or would anyone have any ideas of what might have
> happened, and how to fix?

I don't know why/how it happened, but that is where the source code
for your linux kernel *should* be.

Just as an example, I use the "sys-kernel/gentoo-sources" package for
my kernel source code.  There are many other kernel source packages you
can choose from, but if you have no special reason for using some other
kernel, I suggest you "emerge gentoo-sources" to restore that directory.

Once the kernel source code is restored to /usr/src/linux, you will
need to configure your custom kernel (if you use a customized kernel).

Do you understand what I've said so far?  If not, tell us where you
got lost :)

Re: [gentoo-user] Re: /usr/src/linux gone

[sean]

thanks for the info.
As I said I do not know how this happened, this system has been running
fine for years with little effort  to maintain.

Re: [gentoo-user] Re: /usr/src/linux gone

[Thanasis]

on 03/10/2011 02:29 AM sean wrote the following:
> thanks for the info.
> As I said I do not know how this happened, this system has been running
> fine for years with little effort  to maintain.
Perhaps /usr/src  is/was a mount point?

[gentoo-user] Re: /usr/src/linux gone

[James]

sean <tech.junk <at> myfairpoint.net> writes:



> As I said I do not know how this happened, this system has been running
> fine for years with little effort  to maintain.

Hmmm,
Not a good idea.

Try this page for guidance on upgrading an old installation
of Gentoo:

http://blog.jolexa.net/2009/03/25/gentoo-tips-to-upgrade-your-really-old-installation/


As it was posted recently, and one of my
friends used it as a guide to success....


hth,
James

Re: [gentoo-user] Re: /usr/src/linux gone

[sean]

On Mar 10, 2011, at 8:55 AM, James wrote:

> sean <tech.junk <at> myfairpoint.net> writes:
> 
> 
> 
>> As I said I do not know how this happened, this system has been running
>> fine for years with little effort  to maintain.
> 
> Hmmm,
> Not a good idea.
> 

What I mean by that is that I have had few real problems with it, the system is always kept up to date.

Re: [gentoo-user] Re: /usr/src/linux gone

[sean]

On 03/09/2011 07:01 PM, walt wrote:

> Just as an example, I use the "sys-kernel/gentoo-sources" package for
> my kernel source code.  

I use gentoo-sources as well.

Re: [gentoo-user] /usr/src/linux gone

[Matthew Finkel]

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On Wed, Mar 9, 2011 at 11:29 PM, sean <tech.junk@myfairpoint.net> wrote:

> I just did an update of my system and now the linux directory under
> /usr/src is not there.
> In fact under /usr/src there is nothing.
>
> Something change or would anyone have any ideas of what might have
> happened, and how to fix?
>
>                        Thanks
>                         Sean
>
>
Did you reboot your system and then realize it was empty or did you notice
it was empty after merging the updates?

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Re: [gentoo-user] /usr/src/linux gone

[sean]

On Mar 11, 2011, at 10:08 PM, Matthew Finkel wrote:
> 
> 
> Did you reboot your system and then realize it was empty or did you notice it was empty after merging the updates?

As the updates were running, when it came time to update the nvidia-drivers, a message appeared that it could not find a valid .config in /usr/src/linux
I went to investigate and the linux directory under /usr/src was completely gone.
Fortunately I keep a backup copy of .config.

Re: [gentoo-user] /usr/src/linux gone

[Peter Humphrey]

On Wednesday 09 March 2011 23:29:56 sean wrote:
> I just did an update of my system and now the linux directory under
> /usr/src is not there.
> In fact under /usr/src there is nothing.
> 
> Something change or would anyone have any ideas of what might have
> happened, and how to fix?

I can't help with your problem, but it's odd that I had something similar 
happen the other day. I was making a fresh installation of Gentoo on an 
oldish dual-Opteron box, booting rescue-CD and using two SATA disks with md 
RAID and LVM2. I'd spent the whole afternoon on this, as many steps are 
involved, and I'd eventually reached the installation of GRUB into /boot, 
when I got an error saying that /boot was mounted read-only. On 
investigating, I found that everything I'd put on those two disks had 
disappeared, as though in a puff of smoke. All that was left was the 
underlying partition layout, but with no content. Vanished, without trace, 
just like your kernel tree.

I'm mystified. Oh well, just start again.

So I sympathise with you in your frustration.

-- 
Rgds
Peter

Re: [gentoo-user] /usr/src/linux gone

[Arttu V.]

On 3/12/11, Peter Humphrey <peter@humphrey.ukfsn.org> wrote:
> when I got an error saying that /boot was mounted read-only. On
> investigating, I found that everything I'd put on those two disks had
> disappeared, as though in a puff of smoke. All that was left was the
> underlying partition layout, but with no content. Vanished, without trace,
> just like your kernel tree.

Are we seeing a pattern emerging? Were you possibly installing an
~arch system? And using ext4 or btrfs on the partitions? And emerged
coreutils-8.10 as well?

See the message Mr Jarausch posted yesterday. He referred to this bug as well:

http://bugs.gentoo.org/show_bug.cgi?id=353907

-- 
Arttu V.

Re: [gentoo-user] /usr/src/linux gone

[Peter Humphrey]

On Sunday 13 March 2011 09:34:31 Arttu V. wrote:
> On 3/12/11, Peter Humphrey <peter@humphrey.ukfsn.org> wrote:
> > when I got an error saying that /boot was mounted read-only. On
> > investigating, I found that everything I'd put on those two disks had
> > disappeared, as though in a puff of smoke. All that was left was the
> > underlying partition layout, but with no content. Vanished, without
> > trace, just like your kernel tree.
> 
> Are we seeing a pattern emerging? Were you possibly installing an
> ~arch system? And using ext4 or btrfs on the partitions? And emerged
> coreutils-8.10 as well?

It would be nice to think it was that easy, but no, it was straight amd64 
with coreutils 8.7.

-- 
Rgds
Peter