Gnome hanging and exiting at login.

Gnome hanging and exiting at login.

[Philippe Veber]

Hi all,

I'm using guix on a Debian 12 machine (I installed guix through apt), and
starting recently I can't log in anymore via gdm: after entering my
password the display freezes (blank screen, mouse pointer is displayed but
I can't move it) and after some time I'm back at login screen. If I move
.guix-profile to some other name, everything works correctly.

The thing is, I have no idea how to investigate this. /var/log/gdm3 is
empty, and I don't know whereelse to look. Any idea?

Cheers,
  Philippe.

Re: Gnome hanging and exiting at login.

[Efraim Flashner]

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On Sun, Jan 07, 2024 at 05:44:59PM +0100, Philippe Veber wrote:
> Hi all,
> 
> I'm using guix on a Debian 12 machine (I installed guix through apt), and
> starting recently I can't log in anymore via gdm: after entering my
> password the display freezes (blank screen, mouse pointer is displayed but
> I can't move it) and after some time I'm back at login screen. If I move
> .guix-profile to some other name, everything works correctly.
> 
> The thing is, I have no idea how to investigate this. /var/log/gdm3 is
> empty, and I don't know whereelse to look. Any idea?

Can you share with us a list of the packages you've installed through
Guix?  That might help us find if some environment variable is causing
problems.

Also the output of `guix package --search-paths -p ~/.guix-profile` (or
-p /path/to/where/you/moved/dot-guix-profile).

-- 
Efraim Flashner   <efraim@flashner.co.il>   רנשלפ םירפא
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
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Re: Gnome hanging and exiting at login.

[Philippe Veber]

Thanks Efraim!

Here's what I get:

$guix package --list-installed
python-ete3   3.1.3         out
/gnu/store/wlnq236xg7r30qxljysfv4la0qg3x46y-python-ete3-3.1.3
tracecomp     1.6-1.2661e95 out
/gnu/store/zkym5pzkf9iv47pwcgqmjm78b6s9lyh0-tracecomp-1.6-1.2661e95
coevol         1.6-1.f3f23f0 out
/gnu/store/0qmnqipqrmckd880gfxhlh2359lcd91j-coevol-1.6-1.f3f23f0
r-treeio       1.26.0       out
/gnu/store/17x3b51f35a2dzhzg1kzw4gxc356a4i1-r-treeio-1.26.0
r-tidyverse   2.0.0         out
/gnu/store/8z6bqph9r2920m9ql52piikfv0x07inv-r-tidyverse-2.0.0
r-tidytree     0.4.5         out
/gnu/store/a0s5bqkx7i52cavwp932z5fsmjqxw27j-r-tidytree-0.4.5
r-mvmorph     1.1.9         out
/gnu/store/iz92idl1856rvl45lzybmy78vv8b6idr-r-mvmorph-1.1.9
r-minimal     4.3.2         out
/gnu/store/m1hhz3dqgir7jhk6anb1996pf1j2fbbx-r-minimal-4.3.2
r-ggtreeextra 1.12.0       out
/gnu/store/qdv53igafjgd7xm5pw68vj42w0ij8pyr-r-ggtreeextra-1.12.0
r-ggtree       3.10.0       out
/gnu/store/xjivg7vvljdm3vqzcwjkpas1p64lh117-r-ggtree-3.10.0
r-ggpubr       0.6.0         out
/gnu/store/2kwfwx94si3b82dghyak14kbb6szyb7m-r-ggpubr-0.6.0
r-ggimage     0.3.3         out
/gnu/store/25xr3pzldf5q6z6q2baic5hwaisvcr6h-r-ggimage-0.3.3
r-ggh4x       0.2.6         out
/gnu/store/0mzs0h4di8dazkvf6jbama59wkazzxcd-r-ggh4x-0.2.6
r-guix-install 1.0.0         out
/gnu/store/liihylvgbwkd5s2gvpcvhjp206x98klg-r-guix-install-1.0.0
r-fishdata     1.0.1         out
/gnu/store/r8jnfq3ichak6p1g46dkycayxkz483bq-r-fishdata-1.0.1
r-fsadata     0.4.1         out
/gnu/store/5x4f7qa9y9xb1j046a8g58hc6ccad1f5-r-fsadata-0.4.1

where some of the packages are from custom definitions I wrote. But
checking this list, I immediately suspected python-ete3, which has
dependencies on window manager-related packages :

$guix show python-ete3
name: python-ete3
version: 3.1.3
outputs:
+ out: tout
systems: x86_64-linux
dependencies: python-lxml@4.9.1 python-numpy@1.23.2 python-pyqt@5.15.9
python-pytest@7.1.3 python-scipy@1.10.1
[...]
$guix graph python-ete3 | grep xdg
  "139718079320768" [label = "xdg-utils@1.1.3", shape = box, fontname =
sans];
  "139718079372032" [label = "xdg-user-dirs@0.17", shape = box, fontname =
sans];
  "139718058333568" [label = "xdg-dbus-proxy@0.1.2", shape = box, fontname
= sans];

and indeed, after a guix remove python-ete3, everything's back to normal.

With python-ete3 installed, here's the environment generated by guix:

$guix package --search-paths -p .guix-profile-bck
export PATH="/var/guix/profiles/per-user/pveber/guix-profile/bin"
export
R_LIBS_SITE="/var/guix/profiles/per-user/pveber/guix-profile/site-library/"
export
GUIX_PYTHONPATH="/var/guix/profiles/per-user/pveber/guix-profile/lib/python3.10/site-packages"
export
GI_TYPELIB_PATH="/var/guix/profiles/per-user/pveber/guix-profile/lib/girepository-1.0"
export XDG_DATA_DIRS="/var/guix/profiles/per-user/pveber/guix-profile/share"

Seeing that I tried to fiddle with the variable XDG_DATA_DIRS but I didn't
get anywhere. Let me know if I can give you more details, thanks again!

Le mar. 9 janv. 2024 à 07:49, Efraim Flashner <efraim@flashner.co.il> a
écrit :

> On Sun, Jan 07, 2024 at 05:44:59PM +0100, Philippe Veber wrote:
> > Hi all,
> >
> > I'm using guix on a Debian 12 machine (I installed guix through apt), and
> > starting recently I can't log in anymore via gdm: after entering my
> > password the display freezes (blank screen, mouse pointer is displayed
> but
> > I can't move it) and after some time I'm back at login screen. If I move
> > .guix-profile to some other name, everything works correctly.
> >
> > The thing is, I have no idea how to investigate this. /var/log/gdm3 is
> > empty, and I don't know whereelse to look. Any idea?
>
> Can you share with us a list of the packages you've installed through
> Guix?  That might help us find if some environment variable is causing
> problems.
>
> Also the output of `guix package --search-paths -p ~/.guix-profile` (or
> -p /path/to/where/you/moved/dot-guix-profile).
>
> --
> Efraim Flashner   <efraim@flashner.co.il>   רנשלפ םירפא
> GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
> Confidentiality cannot be guaranteed on emails sent or received unencrypted
>

Re: Gnome hanging and exiting at login.

[Efraim Flashner]

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On Tue, Jan 09, 2024 at 03:00:37PM +0100, Philippe Veber wrote:
> Thanks Efraim!
> 
> Here's what I get:
> 
> $guix package --list-installed
> python-ete3   3.1.3         out
> /gnu/store/wlnq236xg7r30qxljysfv4la0qg3x46y-python-ete3-3.1.3
> tracecomp     1.6-1.2661e95 out
> /gnu/store/zkym5pzkf9iv47pwcgqmjm78b6s9lyh0-tracecomp-1.6-1.2661e95
> coevol         1.6-1.f3f23f0 out
> /gnu/store/0qmnqipqrmckd880gfxhlh2359lcd91j-coevol-1.6-1.f3f23f0
> r-treeio       1.26.0       out
> /gnu/store/17x3b51f35a2dzhzg1kzw4gxc356a4i1-r-treeio-1.26.0
> r-tidyverse   2.0.0         out
> /gnu/store/8z6bqph9r2920m9ql52piikfv0x07inv-r-tidyverse-2.0.0
> r-tidytree     0.4.5         out
> /gnu/store/a0s5bqkx7i52cavwp932z5fsmjqxw27j-r-tidytree-0.4.5
> r-mvmorph     1.1.9         out
> /gnu/store/iz92idl1856rvl45lzybmy78vv8b6idr-r-mvmorph-1.1.9
> r-minimal     4.3.2         out
> /gnu/store/m1hhz3dqgir7jhk6anb1996pf1j2fbbx-r-minimal-4.3.2
> r-ggtreeextra 1.12.0       out
> /gnu/store/qdv53igafjgd7xm5pw68vj42w0ij8pyr-r-ggtreeextra-1.12.0
> r-ggtree       3.10.0       out
> /gnu/store/xjivg7vvljdm3vqzcwjkpas1p64lh117-r-ggtree-3.10.0
> r-ggpubr       0.6.0         out
> /gnu/store/2kwfwx94si3b82dghyak14kbb6szyb7m-r-ggpubr-0.6.0
> r-ggimage     0.3.3         out
> /gnu/store/25xr3pzldf5q6z6q2baic5hwaisvcr6h-r-ggimage-0.3.3
> r-ggh4x       0.2.6         out
> /gnu/store/0mzs0h4di8dazkvf6jbama59wkazzxcd-r-ggh4x-0.2.6
> r-guix-install 1.0.0         out
> /gnu/store/liihylvgbwkd5s2gvpcvhjp206x98klg-r-guix-install-1.0.0
> r-fishdata     1.0.1         out
> /gnu/store/r8jnfq3ichak6p1g46dkycayxkz483bq-r-fishdata-1.0.1
> r-fsadata     0.4.1         out
> /gnu/store/5x4f7qa9y9xb1j046a8g58hc6ccad1f5-r-fsadata-0.4.1
> 
> where some of the packages are from custom definitions I wrote. But
> checking this list, I immediately suspected python-ete3, which has
> dependencies on window manager-related packages :
> 
> $guix show python-ete3
> name: python-ete3
> version: 3.1.3
> outputs:
> + out: tout
> systems: x86_64-linux
> dependencies: python-lxml@4.9.1 python-numpy@1.23.2 python-pyqt@5.15.9
> python-pytest@7.1.3 python-scipy@1.10.1
> [...]
> $guix graph python-ete3 | grep xdg
>   "139718079320768" [label = "xdg-utils@1.1.3", shape = box, fontname =
> sans];
>   "139718079372032" [label = "xdg-user-dirs@0.17", shape = box, fontname =
> sans];
>   "139718058333568" [label = "xdg-dbus-proxy@0.1.2", shape = box, fontname
> = sans];
> 
> and indeed, after a guix remove python-ete3, everything's back to normal.
> 
> With python-ete3 installed, here's the environment generated by guix:
> 
> $guix package --search-paths -p .guix-profile-bck
> export PATH="/var/guix/profiles/per-user/pveber/guix-profile/bin"
> export
> R_LIBS_SITE="/var/guix/profiles/per-user/pveber/guix-profile/site-library/"
> export
> GUIX_PYTHONPATH="/var/guix/profiles/per-user/pveber/guix-profile/lib/python3.10/site-packages"
> export
> GI_TYPELIB_PATH="/var/guix/profiles/per-user/pveber/guix-profile/lib/girepository-1.0"
> export XDG_DATA_DIRS="/var/guix/profiles/per-user/pveber/guix-profile/share"
> 
> Seeing that I tried to fiddle with the variable XDG_DATA_DIRS but I didn't
> get anywhere. Let me know if I can give you more details, thanks again!
> 
> Le mar. 9 janv. 2024 à 07:49, Efraim Flashner <efraim@flashner.co.il> a
> écrit :
> 
> > On Sun, Jan 07, 2024 at 05:44:59PM +0100, Philippe Veber wrote:
> > > Hi all,
> > >
> > > I'm using guix on a Debian 12 machine (I installed guix through apt), and
> > > starting recently I can't log in anymore via gdm: after entering my
> > > password the display freezes (blank screen, mouse pointer is displayed
> > but
> > > I can't move it) and after some time I'm back at login screen. If I move
> > > .guix-profile to some other name, everything works correctly.
> > >
> > > The thing is, I have no idea how to investigate this. /var/log/gdm3 is
> > > empty, and I don't know whereelse to look. Any idea?
> >
> > Can you share with us a list of the packages you've installed through
> > Guix?  That might help us find if some environment variable is causing
> > problems.
> >
> > Also the output of `guix package --search-paths -p ~/.guix-profile` (or
> > -p /path/to/where/you/moved/dot-guix-profile).
> >

It looks like the XDG_DATA_DIRS from the package interfered with the
XDG_DATA_DIRS needed by Debian. I'm not sure I have a suggestion for
that though.

-- 
Efraim Flashner   <efraim@flashner.co.il>   רנשלפ םירפא
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

Re: Gnome hanging and exiting at login.

[Philippe Veber]

Turns out the culprit's not XDG_DATA_DIRS, but GI_TYPELIB_PATH. I don't see
the problem anymore if I comment the line exporting this variable in my
profile.

It seems the issue's been known for some time now:
https://issues.guix.gnu.org/35308
From this issue it seems that there used to be a problem with both
XDG_DATA_DIRS and GI_TYPELIB_PATH, but the fact that only GI_TYPELIB_PATH
generates the problem now suggests that part of the issue has been fixed
(see maybe https://issues.guix.gnu.org/56050).

Unsetting XDG_DATA_DIRS and GI_TYPELIB_PATH in .profile like Nicolas
Goaziou suggested works for me. I still have not a clear idea what should
be done to fix the problem in a satisfying way, but I'm willing to test
suggestions.



Le mer. 10 janv. 2024 à 10:58, Efraim Flashner <efraim@flashner.co.il> a
écrit :

> On Tue, Jan 09, 2024 at 03:00:37PM +0100, Philippe Veber wrote:
> > Thanks Efraim!
> >
> > Here's what I get:
> >
> > $guix package --list-installed
> > python-ete3   3.1.3         out
> > /gnu/store/wlnq236xg7r30qxljysfv4la0qg3x46y-python-ete3-3.1.3
> > tracecomp     1.6-1.2661e95 out
> > /gnu/store/zkym5pzkf9iv47pwcgqmjm78b6s9lyh0-tracecomp-1.6-1.2661e95
> > coevol         1.6-1.f3f23f0 out
> > /gnu/store/0qmnqipqrmckd880gfxhlh2359lcd91j-coevol-1.6-1.f3f23f0
> > r-treeio       1.26.0       out
> > /gnu/store/17x3b51f35a2dzhzg1kzw4gxc356a4i1-r-treeio-1.26.0
> > r-tidyverse   2.0.0         out
> > /gnu/store/8z6bqph9r2920m9ql52piikfv0x07inv-r-tidyverse-2.0.0
> > r-tidytree     0.4.5         out
> > /gnu/store/a0s5bqkx7i52cavwp932z5fsmjqxw27j-r-tidytree-0.4.5
> > r-mvmorph     1.1.9         out
> > /gnu/store/iz92idl1856rvl45lzybmy78vv8b6idr-r-mvmorph-1.1.9
> > r-minimal     4.3.2         out
> > /gnu/store/m1hhz3dqgir7jhk6anb1996pf1j2fbbx-r-minimal-4.3.2
> > r-ggtreeextra 1.12.0       out
> > /gnu/store/qdv53igafjgd7xm5pw68vj42w0ij8pyr-r-ggtreeextra-1.12.0
> > r-ggtree       3.10.0       out
> > /gnu/store/xjivg7vvljdm3vqzcwjkpas1p64lh117-r-ggtree-3.10.0
> > r-ggpubr       0.6.0         out
> > /gnu/store/2kwfwx94si3b82dghyak14kbb6szyb7m-r-ggpubr-0.6.0
> > r-ggimage     0.3.3         out
> > /gnu/store/25xr3pzldf5q6z6q2baic5hwaisvcr6h-r-ggimage-0.3.3
> > r-ggh4x       0.2.6         out
> > /gnu/store/0mzs0h4di8dazkvf6jbama59wkazzxcd-r-ggh4x-0.2.6
> > r-guix-install 1.0.0         out
> > /gnu/store/liihylvgbwkd5s2gvpcvhjp206x98klg-r-guix-install-1.0.0
> > r-fishdata     1.0.1         out
> > /gnu/store/r8jnfq3ichak6p1g46dkycayxkz483bq-r-fishdata-1.0.1
> > r-fsadata     0.4.1         out
> > /gnu/store/5x4f7qa9y9xb1j046a8g58hc6ccad1f5-r-fsadata-0.4.1
> >
> > where some of the packages are from custom definitions I wrote. But
> > checking this list, I immediately suspected python-ete3, which has
> > dependencies on window manager-related packages :
> >
> > $guix show python-ete3
> > name: python-ete3
> > version: 3.1.3
> > outputs:
> > + out: tout
> > systems: x86_64-linux
> > dependencies: python-lxml@4.9.1 python-numpy@1.23.2 python-pyqt@5.15.9
> > python-pytest@7.1.3 python-scipy@1.10.1
> > [...]
> > $guix graph python-ete3 | grep xdg
> >   "139718079320768" [label = "xdg-utils@1.1.3", shape = box, fontname =
> > sans];
> >   "139718079372032" [label = "xdg-user-dirs@0.17", shape = box,
> fontname =
> > sans];
> >   "139718058333568" [label = "xdg-dbus-proxy@0.1.2", shape = box,
> fontname
> > = sans];
> >
> > and indeed, after a guix remove python-ete3, everything's back to normal.
> >
> > With python-ete3 installed, here's the environment generated by guix:
> >
> > $guix package --search-paths -p .guix-profile-bck
> > export PATH="/var/guix/profiles/per-user/pveber/guix-profile/bin"
> > export
> >
> R_LIBS_SITE="/var/guix/profiles/per-user/pveber/guix-profile/site-library/"
> > export
> >
> GUIX_PYTHONPATH="/var/guix/profiles/per-user/pveber/guix-profile/lib/python3.10/site-packages"
> > export
> >
> GI_TYPELIB_PATH="/var/guix/profiles/per-user/pveber/guix-profile/lib/girepository-1.0"
> > export
> XDG_DATA_DIRS="/var/guix/profiles/per-user/pveber/guix-profile/share"
> >
> > Seeing that I tried to fiddle with the variable XDG_DATA_DIRS but I
> didn't
> > get anywhere. Let me know if I can give you more details, thanks again!
> >
> > Le mar. 9 janv. 2024 à 07:49, Efraim Flashner <efraim@flashner.co.il> a
> > écrit :
> >
> > > On Sun, Jan 07, 2024 at 05:44:59PM +0100, Philippe Veber wrote:
> > > > Hi all,
> > > >
> > > > I'm using guix on a Debian 12 machine (I installed guix through
> apt), and
> > > > starting recently I can't log in anymore via gdm: after entering my
> > > > password the display freezes (blank screen, mouse pointer is
> displayed
> > > but
> > > > I can't move it) and after some time I'm back at login screen. If I
> move
> > > > .guix-profile to some other name, everything works correctly.
> > > >
> > > > The thing is, I have no idea how to investigate this. /var/log/gdm3
> is
> > > > empty, and I don't know whereelse to look. Any idea?
> > >
> > > Can you share with us a list of the packages you've installed through
> > > Guix?  That might help us find if some environment variable is causing
> > > problems.
> > >
> > > Also the output of `guix package --search-paths -p ~/.guix-profile` (or
> > > -p /path/to/where/you/moved/dot-guix-profile).
> > >
>
> It looks like the XDG_DATA_DIRS from the package interfered with the
> XDG_DATA_DIRS needed by Debian. I'm not sure I have a suggestion for
> that though.
>
> --
> Efraim Flashner   <efraim@flashner.co.il>   רנשלפ םירפא
> GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
> Confidentiality cannot be guaranteed on emails sent or received unencrypted
>

Gnome hanging and exiting at login.

[Mortimer Cladwell]

This is the same behavior I find on Ubuntu. I was fortunate to correlate it
with the installation of guile-g-golf using guix. If I uninstall g-golf, it
restores normal login behavior. Reinstall g-golf, can't login. Maybe try
uninstalling a guix package related to GTK? gdm?

Mortimer

Re: Gnome hanging and exiting at login.

[Philippe Veber]

Thanks Mortimer, see also my message about unsetting some environment
variables in .profile.

Le jeu. 11 janv. 2024 à 08:41, Mortimer Cladwell <mbcladwell@gmail.com> a
écrit :

> This is the same behavior I find on Ubuntu. I was fortunate to correlate
> it with the installation of guile-g-golf using guix. If I uninstall g-golf,
> it restores normal login behavior. Reinstall g-golf, can't login. Maybe try
> uninstalling a guix package related to GTK? gdm?
>
> Mortimer
>