bug#75157: Grafting inconsistency with multiple outputs is causing problems

bug#75157: Grafting inconsistency with multiple outputs is causing problems

[Dariqq]

Hello,

Yesterday I was playing around with g-golf and libguile and encountered 
some weird glib issues once I linked my c program to glib/gobject.

After asking about this in #guile the problem was discovered to be 2 
different glibs being in use and the workaround is use them with 
'--no-grafts' instead.

I looked into why grafting is causing this problem and here is what I 
have found:

The following happend on guix commit 
e16cdcf37d8223b3634ec5e658356c3b7f154859


Before grafting:
/gnu/store/digl75knygzqg9lrh8adk3pz0qg9cx8h-guile-g-golf-0.8.0-a.1:
Has a reference to: /gnu/store/zgsphhmliwgmjjv1czmbyjql3gk7ynsx-glib-2.78.0
which is the out output of the hidden (@@ (gnu packages glib) glib) package


After applying grafts:
/gnu/store/2ar2h8d7nk3g7c9965y4n68gjr778prk-guile-g-golf-0.8.0-a.1:
Has reference to /gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0

But the hidden glib grafts to
/gnu/store/ls9p0k2chrzviadibzf0iz7rlpkmggms-glib-2.78.0
instead (which is the one I am linking to)


Looking at the grafting derivations the issue seems to be that in one 
case all outputs of glib are grafted and in the other case only the out 
output which leads to the different results.


8<---------------cut here---------------start------------->8---
/gnu/store/ikv0s6dr3yzs398i67vh3p0w8jglxm4w-glib-2.78.0.drv
Derive
([("out","/gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0","","")]
  ,[("/gnu/store/0s4qbdir1j1c6yfnhvj3w4kpplsaafik-pcre2-10.42.drv",["out"])
    ,("/gnu/store/1554x8kqj7xjw5an8rzrnfz3v40spiy7-glibc-2.39.drv",["out"])
    ,("/gnu/store/2c70wagxjjxk8lcj3znrqqlvn2dcj024-glibc-2.39.drv",["out"])
    ,("/gnu/store/523ngwgnmyhszf9mqbk537ka41jbzs00-guile-3.0.9.drv",["out"])
    ,("/gnu/store/7lwb609ira5a3rs9ncxk55azvsnwi6vv-glib-2.78.0.drv",["out"])
    ,("/gnu/store/gmp1ciyg5yna6983phnf22pwsivfanwq-zlib-1.3.drv",["out"])
    ,("/gnu/store/gxn87vb8lb1l3yzmnzidmxbn3nk9x3bf-gcc-11.4.0.drv",["lib"])
  
,("/gnu/store/h268dh05da4jfrl94xq5jkvyic7k2h57-libffi-3.4.4.drv",["out"])
    ,("/gnu/store/h50bkx0qkqj7x0f1sbkgkiszkbdq32qg-zlib-1.3.drv",["out"])
  
,("/gnu/store/hkz1acxfcxil4252qw7i25gcn0f852dw-libffi-3.4.4.drv",["out"])
    ,("/gnu/store/jyki6954ps4gnhpznacfws146svldkpf-gcc-11.4.0.drv",["lib"])
  
,("/gnu/store/vhi205g193z01plb6pbhm75b186zrhis-util-linux-2.37.4.drv",["lib"])
  
,("/gnu/store/w5pgbafd9apavpnczcgblbgmwwp0a8y0-util-linux-2.37.4.drv",["lib"])
    ,("/gnu/store/yni45i1ca3ymb8rna09qh038v102zyjj-pcre2-10.42.drv",["out"])
  
,("/gnu/store/zp7byldvi2imbliv154vv87iai65jwxy-module-import-compiled.drv",["out"])]
  ,["/gnu/store/2mml5mrmhmn1424pymllzk18m2z3l44q-glib-2.78.0-builder","/gnu/store/flaxnn4ciba6wd243ahwgrqw11082imp-module-import"]
  ,"x86_64-linux","/gnu/store/xv4cd7qz4yan93zkjisbmbpxfz78hah2-guile-3.0.9/bin/guile",["--no-auto-compile","-L","/gnu/store/flaxnn4ciba6wd243ahwgrqw11082imp-module-import","-C","/gnu/store/5wdfvn4mklppcg5p9i1d14ksbnsd7m8b-module-import-compiled","/gnu/store/2mml5mrmhmn1424pymllzk18m2z3l44q-glib-2.78.0-builder"]
  ,[("allowSubstitutes","0")
    ,("guix properties","((type . graft) (graft (count . 6)))")
    ,("out","/gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0")
    ,("preferLocalBuild","1")])
--8<---------------cut here---------------end--------------->8---


The "correctly"  grafted glib derivation looks like this:
/gnu/store/xax79x40lzs4wf2v4ipbxvy2gkc9qq7p-glib-2.78.0.drv
8<---------------cut here---------------start------------->8---
gnu/store/xax79x40lzs4wf2v4ipbxvy2gkc9qq7p-glib-2.78.0.drv
Derive
([("bin","/gnu/store/q3d08x70gcjj99k5dd0jbfc8rj97j9lz-glib-2.78.0-bin","","")
  
,("debug","/gnu/store/pn2mdlc86i7x6vrg2j6pslp5sq551255-glib-2.78.0-debug","","")
   ,("out","/gnu/store/ls9p0k2chrzviadibzf0iz7rlpkmggms-glib-2.78.0","","")
  
,("static","/gnu/store/n5s2s4rg3jax3y7kp93bgn2w6s7vlfrz-glib-2.78.0-static","","")]
  ,[("/gnu/store/0s4qbdir1j1c6yfnhvj3w4kpplsaafik-pcre2-10.42.drv",["out"])
    ,("/gnu/store/1554x8kqj7xjw5an8rzrnfz3v40spiy7-glibc-2.39.drv",["out"])
    ,("/gnu/store/2c70wagxjjxk8lcj3znrqqlvn2dcj024-glibc-2.39.drv",["out"])
    ,("/gnu/store/523ngwgnmyhszf9mqbk537ka41jbzs00-guile-3.0.9.drv",["out"])
  
,("/gnu/store/7lwb609ira5a3rs9ncxk55azvsnwi6vv-glib-2.78.0.drv",["bin","debug","out","static"])
    ,("/gnu/store/gmp1ciyg5yna6983phnf22pwsivfanwq-zlib-1.3.drv",["out"])
    ,("/gnu/store/gxn87vb8lb1l3yzmnzidmxbn3nk9x3bf-gcc-11.4.0.drv",["lib"])
  
,("/gnu/store/h268dh05da4jfrl94xq5jkvyic7k2h57-libffi-3.4.4.drv",["out"])
    ,("/gnu/store/h50bkx0qkqj7x0f1sbkgkiszkbdq32qg-zlib-1.3.drv",["out"])
  
,("/gnu/store/hkz1acxfcxil4252qw7i25gcn0f852dw-libffi-3.4.4.drv",["out"])
    ,("/gnu/store/jyki6954ps4gnhpznacfws146svldkpf-gcc-11.4.0.drv",["lib"])
  
,("/gnu/store/piymwc0w49ylyz69ikq6vnj32xhl96h6-bash-minimal-5.1.16.drv",["out"])
  
,("/gnu/store/vhi205g193z01plb6pbhm75b186zrhis-util-linux-2.37.4.drv",["lib"])
  
,("/gnu/store/w5pgbafd9apavpnczcgblbgmwwp0a8y0-util-linux-2.37.4.drv",["lib"])
  
,("/gnu/store/wqa52jpxmv1xiibdxvfls7dnphq83jb5-bash-minimal-5.1.16.drv",["out"])
  
,("/gnu/store/yhxc842f6arm91w4vhdmgazw2nvkn7g7-python-3.10.7.drv",["out"])
  
,("/gnu/store/yig8rg8bjy599m49kia7nph8393x5j2g-python-3.10.7.drv",["out"])
    ,("/gnu/store/yni45i1ca3ymb8rna09qh038v102zyjj-pcre2-10.42.drv",["out"])
  
,("/gnu/store/zp7byldvi2imbliv154vv87iai65jwxy-module-import-compiled.drv",["out"])]
  ,["/gnu/store/65ym8q6k1adkz4d4xalrsdq409r8k8r8-glib-2.78.0-builder","/gnu/store/flaxnn4ciba6wd243ahwgrqw11082imp-module-import"]
  ,"x86_64-linux","/gnu/store/xv4cd7qz4yan93zkjisbmbpxfz78hah2-guile-3.0.9/bin/guile",["--no-auto-compile","-L","/gnu/store/flaxnn4ciba6wd243ahwgrqw11082imp-module-import","-C","/gnu/store/5wdfvn4mklppcg5p9i1d14ksbnsd7m8b-module-import-compiled","/gnu/store/65ym8q6k1adkz4d4xalrsdq409r8k8r8-glib-2.78.0-builder"]
  ,[("allowSubstitutes","0")
    ,("bin","/gnu/store/q3d08x70gcjj99k5dd0jbfc8rj97j9lz-glib-2.78.0-bin")
  
,("debug","/gnu/store/pn2mdlc86i7x6vrg2j6pslp5sq551255-glib-2.78.0-debug")
    ,("guix properties","((type . graft) (graft (count . 8)))")
    ,("out","/gnu/store/ls9p0k2chrzviadibzf0iz7rlpkmggms-glib-2.78.0")
    ,("preferLocalBuild","1")
  
,("static","/gnu/store/n5s2s4rg3jax3y7kp93bgn2w6s7vlfrz-glib-2.78.0-static")])
--8<---------------cut here---------------end--------------->8---



I think it would be good if grafts are only applied per output (which 
might also help resolve #69653).

bug#75157: Grafting inconsistency with multiple outputs is causing problems

[pelzflorian (Florian Pelz)]

Hello Dariqq, your debugging is interesting.

My G-Golf GTK program has a critical error at Gdk-Pixbuf, not GLib at
first sight, but see below.

$ guile /gnu/store/hbf4wqssp0aa0m2cxrwaq0mkxfd5y59p-launcher.scm

(guile:1273): Gtk-WARNING **: 01:21:40.538: Unable to acquire session bus: Failed to execute child process “dbus-launch” (No such file or directory)

(guile:1273): GLib-GObject-CRITICAL **: 01:21:40.586: cannot register existing type 'GdkPixbuf'

(guile:1273): GLib-GObject-CRITICAL **: 01:21:40.586: g_type_add_interface_static: assertion 'G_TYPE_IS_INSTANTIATABLE (instance_type)' failed

(guile:1273): GLib-GObject-CRITICAL **: 01:21:40.586: g_type_add_interface_static: assertion 'G_TYPE_IS_INSTANTIATABLE (instance_type)' failed

(guile:1273): GLib-CRITICAL **: 01:21:40.586: g_once_init_leave: assertion 'result != 0' failed

It cannot register existing type 'GdkPixbuf'.
Bisecting reveals the first bad commit is this:

commit 78c4d00ab02ab41a22058cdbec0329752e47580f
gpg: Signature made Mi 18 Dez 2024 08:27:09 CET
gpg:                using RSA key 27D586A4F8900854329FF09F1260E46482E63562
gpg: Can't check signature: No public key
Author: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date:   Sat Dec 14 22:52:22 2024 +0900

    gnu: glibc: Graft with fix for CVE-2024-2961.
    
    * gnu/packages/base.scm (%glibc-patches): New variable.
    (glibc) [source]: Use it.
    [properties]: Mark CVE-2024-2961 as hidden (resolved).
    [replacement]: Add field to graft with...
    (glibc/fixed): ... this new package.
    
    Fixes: <https://issues.guix.gnu.org/70581>
    Change-Id: I6dd70b0e157283925824348f180c466c2f6387c9

I look at `cat /proc/635/maps`

/gnu/store/1av61zsp5sxs0as48nl52fg78b466r8p-gdk-pixbuf-2.42.10/lib/libgdk_pixbuf-2.0.so.0.4200.10
/gnu/store/1av61zsp5sxs0as48nl52fg78b466r8p-gdk-pixbuf-2.42.10/lib/girepository-1.0/GdkPixbuf-2.0.typelib

and

/gnu/store/10i71f2m5r6rijl8gvn1mpmvzxaxs76l-gdk-pixbuf-2.42.10/lib/libgdk_pixbuf-2.0.so.0.4200.10

this one without a matching typelib, so only the latter was not loaded
through a typelib.

$ guix gc --references /gnu/store/1av61zsp5sxs0as48nl52fg78b466r8p-gdk-pixbuf-2.42.10
/gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0
...
$ guix gc --derivers /gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0
/gnu/store/ikv0s6dr3yzs398i67vh3p0w8jglxm4w-glib-2.78.0.drv
$ guix build /gnu/store/ikv0s6dr3yzs398i67vh3p0w8jglxm4w-glib-2.78.0.drv
/gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0
$ guix gc --references /gnu/store/10i71f2m5r6rijl8gvn1mpmvzxaxs76l-gdk-pixbuf-2.42.10
/gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0
$ guix gc --derivers /gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0
/gnu/store/ikv0s6dr3yzs398i67vh3p0w8jglxm4w-glib-2.78.0.drv
$ guix build /gnu/store/ikv0s6dr3yzs398i67vh3p0w8jglxm4w-glib-2.78.0.drv
/gnu/store/0466q5rlccclzg70f3yprpf9kdvlyfzf-glib-2.78.0


Both my GLibs have one output only.  I still believe above guix commit
is the first bad commit for you, as well, and

guix time-machine -q --commit=78c4d00ab02ab41a22058cdbec0329752e47580f

will show the error and parent commit

guix time-machine -q --commit=08e0144d2338c8fb51e52e74274554583d0faa69

will be fine.  Is it?

I believe what we describe here is yet another symptom of old bug
<https://issues.guix.gnu.org/48907>, but if we have a first bad commit,
and if it is the first bad commit for you, too,
it might help solve it.  Or perhaps this bug can be solved separately if
really the loading through typelib vs. not through typelib is the cause.

Regards,
Florian

bug#75157: Grafting inconsistency with multiple outputs is causing problems

[Dariqq]

Hello FLorian,


I think you are experiencing a different (related) issue because the 
problem I seems to vanish by linking to the glib that is used by g-golf 
instead (the --no-grafts options ensures that only one glib is in my 
guix shell)

On 29.12.24 01:24, pelzflorian (Florian Pelz) wrote:
> 
> 
> Both my GLibs have one output only.  I still believe above guix commit
> is the first bad commit for you, as well, and
> 
> guix time-machine -q --commit=78c4d00ab02ab41a22058cdbec0329752e47580f
> 
> will show the error and parent commit
> 
> guix time-machine -q --commit=08e0144d2338c8fb51e52e74274554583d0faa69
> 
> will be fine.  Is it?
> 



The problem i am seeing is still available in 
08e0144d2338c8fb51e52e74274554583d0faa69.


Here is what I've been playing around with:
a simple c file that just loads a scm file.
a simple scm file that just tries to instantiate a gobject class (in 
this example from json-glib but that is irrelevant, using something 
small and simple)

--8<---------------cut here---------------start------------->8---
main.c:
#include <libguile.h>

int
main (int argc, char **argv)
{
     scm_init_guile();
     scm_c_primitive_load("foo.scm");
}

foo.scm:
(use-modules (g-golf))

(gi-import "Json")

(describe (make <json-parser>
	    #:immutable #t))


Build with
gcc -o main main.c \
     `pkg-config --cflags --libs guile-3.0` \
     `pkg-config --cflags --libs gobject-2.0`

Running this with grafts:
  ./main

(process:3071): GLib-GObject-CRITICAL **: 08:50:36.946: 
g_object_new_is_valid_property: object class 'JsonParser' has no 
property named 'immutable'
#<<json-parser> 7f186b2f56d0> is an instance of class <json-parser>
Slots are:
      g-inst = #<pointer 0x1445e900>

(process:3071): GLib-GObject-CRITICAL **: 08:50:36.947: 
g_object_get_is_valid_property: object class 'JsonParser' has no 
property named 'immutable'

(process:3071): GLib-GObject-CRITICAL **: 08:50:36.947: 
g_object_get_is_valid_property: object class 'JsonParser' has no 
property named 'immutable'
      immutable = #f

When not linking to gobject , using no-grafts or running directly from 
guile repl things work as I would expect:
./main
#<<json-parser> 7ff2471f1d20> is an instance of class <json-parser>
Slots are:
      g-inst = #<pointer 0x2bbbe920>
      immutable = #t
--8<---------------cut here---------------end--------------->8---

On 08e0144d2338c8fb51e52e74274554583d0faa69 a similar problem exists:
g-golf depends on the ungrafted out output of hidden glib
but full glib is getting grafted (because of other other outputs)



If I prepend the glib with the single output graft to pkgconfig path and 
rebuild (s.t. my c prgram is linked to the same glib that is used by 
g-golf) things start magically working again.


> I believe what we describe here is yet another symptom of old bug
> <https://issues.guix.gnu.org/48907>, but if we have a first bad commit,
> and if it is the first bad commit for you, too,
> it might help solve it.  Or perhaps this bug can be solved separately if
> really the loading through typelib vs. not through typelib is the cause.
> 

There might be an even bigger issue here?


However regardless of it causing issues I think having 2 different 
grafted glibs (or rather anything) is not really great.

> Regards,
> Florian

Have nice day,
Dariqq