Updating a very old Guix

Updating a very old Guix

[Konrad Hinsen]

Hi everyone,

I have a computer that I don't use very often, with a rather old Guix
installation from nearly a year ago. So I though I should do an update.

First try: "guix pull".

Does a lot of downloading and compiling, then finishes. But guix no
longer works:

   ERROR: In procedure scm-error:
   no code for module (gcrypt hash)

Next try: I cloned the repository under a different user account (that
still had the old Guix). "guix environment guix", "bootstrap", and
then "configure" get me to the error message:

  configure: error: A recent Guile-SQLite3 could not be found; please
  install it.

But I cannot install a recent Guile-SQLite3 without doing a "guix pull"
first.

One more option I can think of is installing everything required to
compile Guix manually, then compile from source. Not exactly an
attractive idea, all the more since the dependency list in the Guix
manual looks incomplete (it doesn't mention Guile, for example, nor 
Guile-SQLite3).

Are there any other options ? I would like to avoid deleting everything
and starting from scratch because there is one account on that machine
that has in its Guix profile my only working installation of the only
program I actually need this machine for.

Konrad.

Re: Updating a very old Guix

[Julien Lepiller]

Le 2018-11-09 15:37, Konrad Hinsen a écrit :
> Hi everyone,
> 
> I have a computer that I don't use very often, with a rather old Guix
> installation from nearly a year ago. So I though I should do an update.
> 
> First try: "guix pull".
> 
> Does a lot of downloading and compiling, then finishes. But guix no
> longer works:
> 
>    ERROR: In procedure scm-error:
>    no code for module (gcrypt hash)
> 
> Next try: I cloned the repository under a different user account (that
> still had the old Guix). "guix environment guix", "bootstrap", and
> then "configure" get me to the error message:
> 
>   configure: error: A recent Guile-SQLite3 could not be found; please
>   install it.
> 
> But I cannot install a recent Guile-SQLite3 without doing a "guix pull"
> first.
> 
> One more option I can think of is installing everything required to
> compile Guix manually, then compile from source. Not exactly an
> attractive idea, all the more since the dependency list in the Guix
> manual looks incomplete (it doesn't mention Guile, for example, nor
> Guile-SQLite3).
> 
> Are there any other options ? I would like to avoid deleting everything
> and starting from scratch because there is one account on that machine
> that has in its Guix profile my only working installation of the only
> program I actually need this machine for.
> 
> Konrad.

If you have another machine with guix installed, you could try to use 
guix copy to copy a working guix pull profile (~/.config/guix/current) 
to that computer, and then you will be able to use that guix to run guix 
pull. Don't forget to create a key-pair on the other machine and to 
authorize the public key on the receiving end.

So on a machine with a recent guix:

guix archive --generate-key
scp /etc/guix/signing-key.pub remote@machine

On the first machine:

guix archive --authorize < signing-key.pub

On the machine with a recent guix:

guix copy --to=remote@machine `readlink -f ~/.config/guix/latest`

And finally on the machine with an old guix:

/gnu/store/.../bin/guix pull
# with ... the result of readlink on the machine with the recent guix.

Hopefully, that will work :)

See 
http://guix.info/manual/en/Invoking-guix-copy.html#Invoking-guix-copy 
and 
http://guix.info/manual/en/Invoking-guix-archive.html#Invoking-guix-archive 
for reference.

Re: Updating a very old Guix

[swedebugia]

Hi!

On 2018-11-09 15:37, Konrad Hinsen wrote:
> First try: "guix pull".

Have you tried the commit for the next nearest stable? v.0.13 v.0.14 
v.0.15? (gcrypt was added after 0.15 point)
Ludo recommended in another thread to pull in increments. But basically 
building guix with an old guix is not supported at all ATM but should work.

Please report your progress! I will work on improving the pull-section 
of the manual shortly.

>     ERROR: In procedure scm-error:
>     no code for module (gcrypt hash)
Se my solution here:

https://gitlab.com/swedebugia/guix-notes/blob/master/BUILD_LATEST_GUIX_FROM_SOURCE_WITH_Guix_v0.15.org

(search for "gcrypt")

-- 
Cheers
Swedebugia

Re: Updating a very old Guix

[Konrad Hinsen]

Hi Swedebugia and Julien,

First of all, thanks to both of you for your suggestions!

> Have you tried the commit for the next nearest stable? v.0.13 v.0.14 
> v.0.15? (gcrypt was added after 0.15 point)
> Ludo recommended in another thread to pull in increments. But basically 
> building guix with an old guix is not supported at all ATM but should work.

I did consider going through intermediates, but only when the problems
showed up. Since I do not have a working Guix any more, I cannot use
"guix pull" with a commit to move to an intermediate.

I can still check out some intermediate version and build from source.
But then I guess I would have to install it in some temporary place, and
use it to build another intermediate. In the end, I would use the final
one to do a pull on my standard user account. Well, that just *might*
work...

> Please report your progress!

I will!


> If you have another machine with guix installed, you could try to use 
> guix copy to copy a working guix pull profile (~/.config/guix/current) 

Yes, I do have another machine with a pretty recent Guix. Unfortunately
I have no access to it over the weekend, but if the above strategy
fails, I will try yours next week.

Thanks again to both of you,
  Konrad

Re: Updating a very old Guix

[znavko]

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Hello! It is interesting to read. I use GuixSD for 2 months. I have not accumulated problems and solutions, but an issue with gcrypt and hash appeared here. 
The luck was there, I only can show you a link: http://lists.gnu.org/archive/html/bug-guix/2018-09/msg00153.html <http://lists.gnu.org/archive/html/bug-guix/2018-09/msg00153.html>
I think the main feature of guix - the roll back function - rests there. 
May be you could choose most previous kernel in grub and then ran
`guix system roll-back`. Would it repair your system?


9. Nov 2018 20:07 by konrad.hinsen@fastmail.net <mailto:konrad.hinsen@fastmail.net>:


> Hi Swedebugia and Julien,
>
> First of all, thanks to both of you for your suggestions!
>
>> Have you tried the commit for the next nearest stable? v.0.13 v.0.14 
>> v.0.15? (gcrypt was added after 0.15 point)
>> Ludo recommended in another thread to pull in increments. But basically 
>> building guix with an old guix is not supported at all ATM but should work.
>
> I did consider going through intermediates, but only when the problems
> showed up. Since I do not have a working Guix any more, I cannot use
> "guix pull" with a commit to move to an intermediate.
>
> Thanks again to both of you,
>   Konrad

[-- Attachment #2: Type: text/html, Size: 1706 bytes --]

Re: Updating a very old Guix

[Konrad Hinsen]

Konrad Hinsen <konrad.hinsen@fastmail.net> writes:

> I can still check out some intermediate version and build from source.

I can indeed check out and build them, but not use them at all. The
binaries for these intermediate versions are no longer on the substitute
servers, and my machine runs out of memory and/or disk space when trying
to rebuild everything from source.

So I will try Julien's suggestion next week.

Konrad.

Re: Updating a very old Guix

[Konrad Hinsen]

<znavko@tutanota.com> writes:

> I think the main feature of guix - the roll back function - rests there. 
> May be you could choose most previous kernel in grub and then ran
> `guix system roll-back`. Would it repair your system?

Sorry for my lack of precision: I am not running GuixSD, but the guix
package manager on top of a Debian installation.

Konrad.

Re: Updating a very old Guix

[swedebugia]

Hi

On 2018-11-09 18:07, Konrad Hinsen wrote:
> Hi Swedebugia and Julien,
>
> First of all, thanks to both of you for your suggestions!
>
>> Have you tried the commit for the next nearest stable? v.0.13 v.0.14
>> v.0.15? (gcrypt was added after 0.15 point)
>> Ludo recommended in another thread to pull in increments. But basically
>> building guix with an old guix is not supported at all ATM but should work.
> I did consider going through intermediates, but only when the problems
> showed up. Since I do not have a working Guix any more, I cannot use
> "guix pull" with a commit to move to an intermediate.

This is most probably not correct. You most probably do have a working 
Guix in the store but your current guix points to the new one which 
lacks guile-gcrypt.

I suggest you roll back your guix pull profile following the manual. 
(this might not work if your guix is too old)
https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-pull.html#Invoking-guix-pull

If you want more help I suggest you run:

$ guile --version | head -1 && guix --version | head -1

And your env
$ env

Also
guix package -l && guix pull -l
ls -l ~/.guix-profile ~/.config/guix/
-- 
Cheers Swedebugia

Re: Updating a very old Guix

[Konrad Hinsen]

swedebugia <swedebugia@riseup.net> writes:

> This is most probably not correct. You most probably do have a working 
> Guix in the store but your current guix points to the new one which 
> lacks guile-gcrypt.

Indeed, kind of. It looks more complicated than that.

As you say, there is indeed a working guix in the store, but calling
apparently still makes it use the messed-up code under ~/.config/guix.
After renaming this to move it out of the way, I can again run guix
commands.

However...

> I suggest you roll back your guix pull profile following the manual. 
> (this might not work if your guix is too old)

My guix does seem to be too old for that. And while I can now invoke it
without an immediate error message, every attempt at installing or even
removing packages leads to an attempt to compile the GCC toolchain,
which fails for lack of disk space (there's only one 10 GB partition).


So I tried Julien's suggestion to copy over a newer guix from another
machine.

Step by step:

   guix archive --generate-key

Works fine, but must be run as root because it writes to /etc.

   scp /etc/guix/signing-key.pub remote@machine

then on the remote machine

   guix archive --authorize < signing-key.pub

Again "guix archive" must be run as root. Back to the "new-guix" machine:

   guix copy --to=remote@machine `readlink -f ~/.config/guix/latest`

guix copy: error: failed to connect to `#<input-output: channel (open)
c7ed00>': Protocol error

Hard to say which protocol is not respected there, but given how old my
guix is, I suspect the protocol used by "guix copy" has changed since.

So let's try a variant: use "guix archive" to export a nar file, copy it
over to the other machine, and import it.

   guix archive --export `readlink -f ~/.config/guix/latest` > guix-update.nar

guix archive: error: build failed: program `guix-authenticate' failed
with exit code 1

There isn't much documentation on "guix authenticate" and how it might
fail, so I'll end my experiments here. Does anyone have an idea for
something else that I might try?

Cheers,
  Konrad.

Re: Updating a very old Guix

[Julien Lepiller]

Le 2018-11-13 13:43, Konrad Hinsen a écrit :
> swedebugia <swedebugia@riseup.net> writes:
> 
>> This is most probably not correct. You most probably do have a working
>> Guix in the store but your current guix points to the new one which
>> lacks guile-gcrypt.
> 
> Indeed, kind of. It looks more complicated than that.
> 
> As you say, there is indeed a working guix in the store, but calling
> apparently still makes it use the messed-up code under ~/.config/guix.
> After renaming this to move it out of the way, I can again run guix
> commands.
> 
> However...
> 
>> I suggest you roll back your guix pull profile following the manual.
>> (this might not work if your guix is too old)
> 
> My guix does seem to be too old for that. And while I can now invoke it
> without an immediate error message, every attempt at installing or even
> removing packages leads to an attempt to compile the GCC toolchain,
> which fails for lack of disk space (there's only one 10 GB partition).
> 
> 
> So I tried Julien's suggestion to copy over a newer guix from another
> machine.
> 
> Step by step:
> 
>    guix archive --generate-key
> 
> Works fine, but must be run as root because it writes to /etc.
> 
>    scp /etc/guix/signing-key.pub remote@machine
> 
> then on the remote machine
> 
>    guix archive --authorize < signing-key.pub
> 
> Again "guix archive" must be run as root. Back to the "new-guix" 
> machine:
> 
>    guix copy --to=remote@machine `readlink -f ~/.config/guix/latest`
> 
> guix copy: error: failed to connect to `#<input-output: channel (open)
> c7ed00>': Protocol error
> 
> Hard to say which protocol is not respected there, but given how old my
> guix is, I suspect the protocol used by "guix copy" has changed since.
> 
> So let's try a variant: use "guix archive" to export a nar file, copy 
> it
> over to the other machine, and import it.
> 
>    guix archive --export `readlink -f ~/.config/guix/latest` > 
> guix-update.nar

The command you should run is:

guix archive --recursive --export `readlink -f ~/.config/guix/current` > 
guix-update.nar

note the --recursive (so guix can find its dependencies, but it will 
bundle every dependency in the .nar, so there may be some duplication 
that guix copy would have avoided), and the actual directory name is 
current, not latest (latest is the old name of the guix installation 
directory, but since we switched to full profiles for guix, we also 
renamed the directory where the current guix version is installed). I 
think I told you "latest" before, that was my mistake, sorry. Maybe you 
can try again "guix copy", with "current" this time?

> 
> guix archive: error: build failed: program `guix-authenticate' failed
> with exit code 1
> 
> There isn't much documentation on "guix authenticate" and how it might
> fail, so I'll end my experiments here. Does anyone have an idea for
> something else that I might try?
> 
> Cheers,
>   Konrad.

Re: Updating a very old Guix

[Konrad Hinsen]

Hi Julien,

> The command you should run is:
>
> guix archive --recursive --export `readlink -f ~/.config/guix/current` > 
> guix-update.nar
>
> note the --recursive (so guix can find its dependencies, but it will 
> bundle every dependency in the .nar, so there may be some duplication 

I just tried that one - same problem with guix-authenticate.

> renamed the directory where the current guix version is installed). I 
> think I told you "latest" before, that was my mistake, sorry. Maybe you 
> can try again "guix copy", with "current" this time?

No change, I get the same protocol error.

I actually do have ~/.config/guix/latest (probably left over from an
older guix), and it does point to a store entry. So I should be able to
archive and copy it, even if it's not the entry that I need.

Cheers,
  Konrad.

Re: Updating a very old Guix

[swedebugia]

Hi

On 2018-11-13 13:43, Konrad Hinsen wrote:

snip

> 
> So let's try a variant: use "guix archive" to export a nar file, copy it
> over to the other machine, and import it.
> 
>     guix archive --export `readlink -f ~/.config/guix/latest` > guix-update.nar
> 
> guix archive: error: build failed: program `guix-authenticate' failed
> with exit code 1

Interesting bug!

Could you report this to bug-guix@gnu.org?
this code runs on the daemon so any detailed errors will probably be in 
the daemon log.

we need the version of your guix (and your daemon) so we can reproduce it.

guix-authenticate uses gcrypt which was recently changed by ludo to 
guile-gcrypt so this might have introduced a regression.

> 
> There isn't much documentation on "guix authenticate" and how it might
> fail, so I'll end my experiments here. Does anyone have an idea for
> something else that I might try?

How about reinstalling v. 0.15 overwriting your current installation?

this would invalidate all your store items though.

-- 
Cheers
Swedebugia

Re: Updating a very old Guix

[Konrad Hinsen]

swedebugia <swedebugia@riseup.net> writes:

> Could you report this to bug-guix@gnu.org?

Done (and Ludo and Ricardo are already looking into this).

> How about reinstalling v. 0.15 overwriting your current installation?
>
> this would invalidate all your store items though.

Exactly, which is why I would like to avoid it. The current profile
of the only account that matters on that machine contains some fragile
software, so I am not at all sure that if I reinstall and update
everything I will still have a working system.

Perhaps I could try to archive all the stuff in the profile, re-install
Guix, and recover my store items from the archive. But as far as I know
there is no way to install them into a profile afterwards.

BTW, I did find a way to run "guix pull" which has a good chance to work
on a more typical installation: remove $HOME/.config/guix and then run
"/usr/local/bin/guix pull". Unfortunately, this fails on my machine
because of insufficient disk space for building an enormous amount of
packages. Even gtk, although I am on a headless server.

I actually wonder if it is reasonable to run Guix on such a limited
machine. My store fills up 1/3 of the 10 GB partition, and that's right
after a "guix gc". Perhaps I should keep a profile with that machine's
software on my main Guix machine and just copy over the binaries from
time to time.

Konrad.

Re: Updating a very old Guix

[swedebugia]

[-- Attachment #1: Type: text/plain, Size: 1018 bytes --]

On 2018-11-14 16:21, Konrad Hinsen wrote:

snip

> BTW, I did find a way to run "guix pull" which has a good chance to work
> on a more typical installation: remove $HOME/.config/guix and then run
> "/usr/local/bin/guix pull". Unfortunately, this fails on my machine
> because of insufficient disk space for building an enormous amount of
> packages. Even gtk, although I am on a headless server.

GTK? Interesting. Could you share your package profile (guix package -I) 
and config.scm?

I run GuixSD 0.15 in Qemu on a 10GB cow. The attached config.scm and the 
following packages consumes ~3.2GB space in the store:
sdb@komputilo ~/guix-tree [env]$ guix package -I |awk '{ print $1 " " $2 }'
openssh 7.7p1
nss 3.36.1
file 5.32
wget 1.19.5
git 2.18.0
git:send-email 2.18.0
guile-readline 2.2.3
emacs-guix 0.4.1.1
emacs-no-x 26.1
tree 1.7.0
emacs-paredit 24
geiser 0.10
magit 2.13.0
emacs-yasnippet 0.12.2
recutils 1.7

I never had to build anything. All substitutes needed have been available.

-- 
Cheers
Swedebugia

[-- Attachment #2: config.scm --]
[-- Type: text/x-scheme, Size: 2371 bytes --]

;; This is an operating system configuration template
;; for a "bare bones VM" setup, with no X11 display server
;; and working HTTPS.

(use-modules (gnu))
(use-service-modules networking ssh)
(use-package-modules screen ssh certs)

(operating-system
  (host-name "komputilo")
  (timezone "Europe/Berlin")
  (locale "en_US.utf8")

  ;; Boot in "legacy" BIOS mode, assuming /dev/vdX is the
  ;; target hard disk specified in the VM, and "my-root" 
  ;; is the label of the target root file system.
  (bootloader (bootloader-configuration
                (bootloader grub-bootloader)
                (target "/dev/vda")
		(terminal-outputs '(console))))
  (file-systems (cons (file-system
			;; Hint: set label with the "e2label" command.
                        (device (file-system-label "my-root"))
                        (mount-point "/")
                        (type "ext4"))
                      %base-file-systems))

  ;; This is where user accounts are specified.  The "root"
  ;; account is implicit, and is initially created with the
  ;; empty password.
  (users (cons (user-account
                (name "sdb")
                (comment "Bob's sister")
                (group "users")

                ;; Adding the account to the "wheel" group
                ;; makes it a sudoer.  Adding it to "audio"
                ;; and "video" allows the user to play sound
                ;; and access the webcam.
                (supplementary-groups '("wheel"
                                        "audio" "video"))
                (home-directory "/home/sdb"))
               %base-user-accounts))

  ;; Globally-installed packages.
  (packages (cons* 	screen 
			openssh 	; For SSH daemon
			nss-certs	; Needed for HTTPS to work 
			%base-packages))

  ;; Add services to the baseline: a DHCP client and
  ;; an SSH server.
  (services (cons* (dhcp-client-service)		; Aquire IP via DHCP from Qemu on boot
                   (service openssh-service-type	; SSH server started on boot
                            (openssh-configuration
                              (port-number 22)))
		   (modify-services %base-services      ; Add berlin as first priority substitute server
				    (guix-service-type config =>
						       (guix-configuration
							(inherit config)
							(substitute-urls '("https://berlin.guixsd.org https://mirror.hydra.gnu.org"))))))))

Re: Updating a very old Guix

[Konrad Hinsen]

swedebugia <swedebugia@riseup.net> writes:

> GTK? Interesting. Could you share your package profile (guix package -I) 
> and config.scm?

The profile, yes, see below. both for my standard user account and for
root.  But no config.scm, I am not running GuixSD but Guix on top of
Debian.

You will see that my profile contains guix itself, which as to my
current understanding is not a good idea. I tried to remove it, but I
cannot even do "guix package -r guix" without compiling half of the free
software known in this universe. Including, once more, GTK, which is
probably a dependency of Emacs, but that's not a reason to compile GTK
for removing a package. It kind of looks like guix rebuilds all the
remaining stuff in my profile, which should not be necessary.

I realize of course that I am complaining about the performance of a
very old guix!

Cheers,
  Konrad.

My plain user profile:

Generation 42	Mar 23 2018 09:13:29	(current)
  python	3.6.3	out	/gnu/store/6zwqlrzz12sjnp06nh807kmy5q3zymwl-python-3.6.3
  r	3.4.3	out	/gnu/store/fjci8mjl3n05jjxfsxdh682qwkxb6qcr-r-3.4.3
  emacs-htmlize	1.51	out	/gnu/store/jd40vhyhwgf1afjnpvj33p9y1pb0sbd0-emacs-htmlize-1.51
  emacs-dash	2.13.0	out	/gnu/store/l3y1bkv4jhw7hgi552cafc0c70r2nk2m-emacs-dash-2.13.0
  emacs	25.3	out	/gnu/store/cajd1fkarcm002zcgfzl5i3gmmam2ry1-emacs-25.3
  syncthing	0.14.45	out	/gnu/store/iisxxp8wydi16nvz4xbh78s1lpliv01y-syncthing-0.14.45
  vdirsyncer	0.16.4	out	/gnu/store/i0w1vks78drwifgg2lqpzs0s8hd8yx0b-vdirsyncer-0.16.4
  unzip	6.0	out	/gnu/store/isp3x3aaviiivbh7vlvifh62dj3dqkzb-unzip-6.0
  mosh	1.3.2	out	/gnu/store/8gzqkya3wsvavlmdbc9c82xg4p78xpyh-mosh-1.3.2
  mercurial	4.4.1	out	/gnu/store/yc3fw4yfhxmsz2agi7cr83fn70fq2a7c-mercurial-4.4.1
  git	2.16.2	out	/gnu/store/d5l2wfccmyr817glb8vlavwkmx67p0qn-git-2.16.2
  nss-certs	3.35	out	/gnu/store/d48rkmvrbzaabxdldcrdps7cf27rm092-nss-certs-3.35
  glibc-locales	2.26.105-g0890d5379c	out	/gnu/store/j73ld7v624ix39imy94bncxzl8nirdn8-glibc-locales-2.26.105-g0890d5379c
  guix	0.14.0-9.bdf0c64	out	/gnu/store/3abjgr7dws69089lrfkf0n92qww1946j-guix-0.14.0-9.bdf0c64

Generation 43	Mar 26 2018 16:54:09
 - emacs-dash	2.13.0	out	/gnu/store/l3y1bkv4jhw7hgi552cafc0c70r2nk2m-emacs-dash-2.13.0
 - emacs-htmlize	1.51	out	/gnu/store/jd40vhyhwgf1afjnpvj33p9y1pb0sbd0-emacs-htmlize-1.51


The root profile:

Generation 1	Nov 29 2017 11:46:40
  guix	0.13.0	out	/gnu/store/vir3lrwqy50pr8fkaf3m091dgbrja2n6-guix-0.13.0
  glibc-utf8-locales	2.25	out	/gnu/store/g4g0zhcp5j9pyjmcv02ks4x2b48k252x-glibc-utf8-locales-2.25
  glibc	2.25	out	/gnu/store/rmjlycdgiq8pfy5hfi42qhw3k7p6kdav-glibc-2.25

Generation 2	Nov 29 2017 11:55:00
 + hello	2.10	out	/gnu/store/prvjrj6i8cz7rvkgm643h952bv2daj1h-hello-2.10

Generation 3	Nov 29 2017 11:56:11
 - hello	2.10	out	/gnu/store/prvjrj6i8cz7rvkgm643h952bv2daj1h-hello-2.10

Generation 4	Dec 07 2017 16:37:34	(current)
 + glibc	2.25	out	/gnu/store/38kr8xi7nib8rx8xr4gi0w0d8knyca3k-glibc-2.25
 + glibc-utf8-locales	2.25	out	/gnu/store/xa391b23r5lbwxb9q26sq5rq1fkd1xi3-glibc-utf8-locales-2.25
 + guix	0.13.0-13.3fb6464	out	/gnu/store/sy84f3kbjj2f2nl1ljbdcmsqrz8j8nqn-guix-0.13.0-13.3fb6464
 - glibc	2.25	out	/gnu/store/rmjlycdgiq8pfy5hfi42qhw3k7p6kdav-glibc-2.25
 - glibc-utf8-locales	2.25	out	/gnu/store/g4g0zhcp5j9pyjmcv02ks4x2b48k252x-glibc-utf8-locales-2.25
 - guix	0.13.0	out	/gnu/store/vir3lrwqy50pr8fkaf3m091dgbrja2n6-guix-0.13.0