Arch Linux

dax79

Member

Registered: 2021-12-28

Posts: 18

[SOLVED]Failed to check for chroot() environment: Permission denied

Hi, on my archlinux fully update pc when i run pacman -Syu i get a lot of

Failed to check for chroot() environment: Permission denied

This happen after a resize/moving hard disk partition through gparted.
I also tried to search the web but without results.
Can somebody give me a start point for further investigation?
Thanks
Davide

Last edited by dax79 (Yesterday 21:28:20)

noesoespanol

Member

Registered: 2026-03-30

Posts: 9

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

It could be incorrect or overly restrictive mount options on your root. Try "mount | grep -E ' / | /boot | /home'" to check current mount options, or "cat /etc/fstab" to check what fstab says. Also "ls -ld / /boot /var/cache/pacman/pkg", have a look at permissions. Look for noexec, nosuid, or nodev on the root (/) filesystem?

Remount root with proper options temporarily:

sudo mount -o remount,exec,suid,dev /

Edit fstab:

sudo nano /etc/fstab

Make sure the root line looks like this (adjust UUID or PARTUUID):

UUID=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx / ext4 defaults 0 1

Remove any noexec, nosuid, nodev from the root / line, but for /boot or EFI partition, defaults or noatime is usually fine. I use noatime myself. Less "junk" imho. Example for root: defaults,noatime (no noexec etc.).

I use BTRFS though, so mine looks like:

<idiiii>    /    btrfs        defaults,rw,noatime,compress=zstd:3,ssd,space_cache=v2    0 0

Test fstab and see: "sudo mount -a"

dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Thanks

mount | grep -E ' / | /boot | /home'
/dev/sda1 on / type ext4 (rw,relatime)

ls -ld / /boot /var/cache/pacman/pkg
drwxr-xr-x 18 root root    4096 21 apr 11.12 /
drwxr-xr-x  3 root root    4096 21 apr 09.20 /boot
drwxr-xr-x  2 root root 2949120 21 apr 09.12 /var/cache/pacman/pkg

cat /etc/fstab
# 
# /etc/fstab: static file system information
#
# <file system>	<dir>	<type>	<options>	<dump>	<pass>
# /dev/sda1
UUID=2984ab62-e531-426e-bc0f-98ee18ea2c57	/         	ext4      	rw,relatime,data=ordered	0 1

# /dev/sda5
UUID=39e6a40e-dd1f-49ff-b790-189ea4fff4dd	swap      	swap      	defaults  	0 0

/dev/sda6    /media/Dati 	ntfs-3g silent,umask=0,locale=it_IT.utf8 0 0

What i have to remove from /etc/fstab?

blkid 
/dev/sda1: UUID="2984ab62-e531-426e-bc0f-98ee18ea2c57" BLOCK_SIZE="4096" TYPE="ext4" PARTUUID="56d66567-01"
/dev/sda5: UUID="39e6a40e-dd1f-49ff-b790-189ea4fff4dd" TYPE="swap" PARTUUID="56d66567-05"
/dev/sda6: LABEL="Dati" BLOCK_SIZE="512" UUID="2EFDD8F202E377AA" TYPE="ntfs" PARTUUID="56d66567-06"

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

This happen after a resize/moving hard disk partition through gparted.

What partitions exactly?
I assume there's also a parallel windows installation?

lsblk -f
sudo fdisk -l /dev/sda
df -h
sudo LC_ALL=C pacman -Qkk | grep -v ', 0 altered files' | grep -v backup

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

What partitions exactly?

Honestly i don' t remember, six months ago...

I assume there's also a parallel windows installation?

Nope

lsblk -f
NAME   FSTYPE FSVER LABEL UUID                                 FSAVAIL FSUSE% MOUNTPOINTS
sda                                                                           
├─sda1 ext4   1.0         2984ab62-e531-426e-bc0f-98ee18ea2c57  148,5G    35% /
├─sda2                                                                        
├─sda5 swap   1           39e6a40e-dd1f-49ff-b790-189ea4fff4dd                [SWAP]
└─sda6 ntfs         Dati  2EFDD8F202E377AA                      212,7G    52% /media/Dati
sr0

sudo fdisk -l /dev/sda
fdisk -l /dev/sda
Disk /dev/sda: 931,51 GiB, 1000204886016 bytes, 1953525168 sectors
Disk model: ST31000524AS    
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x56d66567

Dispositivo Avvio     Start       Fine   Settori   Size Id Tipo
/dev/sda1              2048  531361791 531359744 253,4G 83 Linux
/dev/sda2         531361792 1457274879 925913088 441,5G  5 Esteso
/dev/sda5         531363840  535664639   4300800   2,1G 82 Linux swap / Solaris
/dev/sda6         535666688 1457274879 921608192 439,5G  7 HPFS/NTFS/exFAT

df -h
File system     Dim. Usati Dispon. Uso% Montato su
/dev/sda1       250G   89G    149G  38% /
devtmpfs        1,9G     0    1,9G   0% /dev
tmpfs           1,9G     0    1,9G   0% /dev/shm
tmpfs           776M  1,2M    775M   1% /run
none            1,0M     0    1,0M   0% /run/credentials/systemd-journald.service
tmpfs           1,9G  4,0K    1,9G   1% /tmp
/dev/sda6       440G  227G    213G  52% /media/Dati
none            1,0M     0    1,0M   0% /run/credentials/getty@tty1.service
tmpfs           388M  108K    388M   1% /run/user/1000

LC_ALL=C pacman -Qkk | grep -v ', 0 altered files' | grep -v backup
LC_ALL=C pacman -Qkk | grep -v ', 0 altered files' | grep -v backup
warning: accountsservice: /var/lib/AccountsService (Permissions mismatch)
warning: cups: /etc/cups/classes.conf (Permissions mismatch)
warning: cups: /etc/cups/printers.conf (Permissions mismatch)
warning: cups: /etc/cups/subscriptions.conf (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/lang (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/plugins (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/plugins/audio (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/plugins/bearer (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/plugins/imageformats (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/plugins/platforms (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/plugins/printsupport (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/flightsim (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/flightsim/aircraft (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/flightsim/controller (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/flightsim/hud (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/flightsim/keyboard (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/flightsim/planet (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/resources/gdal (Permissions mismatch)
warning: google-earth-pro: /opt/google/earth/pro/shaders (Permissions mismatch)
warning: hplip-plugin: /var/lib/hp (GID mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Modification time mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Modification time mismatch)
warning: libutempter: /usr/lib/utempter/utempter (GID mismatch)
warning: libutempter: /usr/lib/utempter/utempter (Permissions mismatch)
warning: libvlc: /usr/lib/vlc/plugins/plugins.dat (Modification time mismatch)
warning: libvlc: /usr/lib/vlc/plugins/plugins.dat (Size mismatch)
warning: libvlc: /usr/lib/vlc/plugins/plugins.dat (SHA256 checksum mismatch)
warning: nginx-mainline: /var/lib/nginx/proxy (UID mismatch)
accountsservice: 298 total files, 1 altered file
cups: 947 total files, 3 altered files
google-earth-pro: 417 total files, 16 altered files
hplip-plugin: 50 total files, 1 altered file
java-runtime-common: 21 total files, 2 altered files
libutempter: 20 total files, 1 altered file
libvlc: 120 total files, 1 altered file
nginx-mainline: 47 total files, 1 altered file
warning: samba: /var/lib/samba/private (Permissions mismatch)
warning: shadow: /usr/bin/groupmems (GID mismatch)
warning: shadow: /usr/bin/groupmems (Permissions mismatch)
warning: systemd: /var/log/journal (GID mismatch)
samba: 1196 total files, 1 altered file
shadow: 576 total files, 1 altered file
systemd: 1826 total files, 1 altered file

Thanks

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Doesn't look horribly broken
So let's see what this

Hi, on my archlinux fully update pc when i run pacman -Syu i get a lot of

actually is resp. where it's coming from.

sudo pacman -Syu --debug | tee /tmp/pacman.out
cat /tmp/pacman.out | curl -s -H "Accept: application/json, */*" --upload-file - 'https://paste.c-net.org/'

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Thanks seth
Paste.c Link

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Seems this is coming from the systemd hooks, does

sudo systemctl daemon-reload

cause this?

stat: cannot statx '/proc/1/root': Permesso negato

https://bbs.archlinux.org/viewtopic.php … 1#p1981431 ?
What is the context here?

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Seems this is coming from the systemd hooks, does

sudo systemctl daemon-reload

cause this?

stat: cannot statx '/proc/1/root': Permesso negato

No

[root@dax-arch davide]# systemctl daemon-reload
[root@dax-arch davide]# 

https://bbs.archlinux.org/viewtopic.php … 1#p1981431 ?
What is the context here?

I read the thread before post, this is mine

cat /etc/pacman.conf
#
# /etc/pacman.conf
#
# See the pacman.conf(5) manpage for option and repository directives

#
# GENERAL OPTIONS
#
[options]
# The following paths are commented out with their default values listed.
# If you wish to use different paths, uncomment and update the paths.
#RootDir     = /
#DBPath      = /var/lib/pacman/
#CacheDir    = /var/cache/pacman/pkg/
#LogFile     = /var/log/pacman.log
#GPGDir      = /etc/pacman.d/gnupg/
#HookDir     = /etc/pacman.d/hooks/
HoldPkg     = pacman glibc
#XferCommand = /usr/bin/curl -C - -f %u > %o
#XferCommand = /usr/bin/wget --passive-ftp -c -O %o %u
#CleanMethod = KeepInstalled
#UseDelta    = 0.7
Architecture = auto

# Pacman won't upgrade packages listed in IgnorePkg and members of IgnoreGroup
#IgnorePkg   = nvidia-390xx
#IgnorePkg   = nvidia-390xx-utils
#IgnoreGroup =

#NoUpgrade   =
#NoExtract   =

# Misc options
#UseSyslog
#Color
#TotalDownload
CheckSpace
VerbosePkgLists

# By default, pacman accepts packages signed by keys that its local keyring
# trusts (see pacman-key and its man page), as well as unsigned packages.
SigLevel    = Required DatabaseOptional
LocalFileSigLevel = Optional
#RemoteFileSigLevel = Required

# NOTE: You must run `pacman-key --init` before first using pacman; the local
# keyring can then be populated with the keys of all official Arch Linux
# packagers with `pacman-key --populate archlinux`.

#
# REPOSITORIES
#   - can be defined here or included from another file
#   - pacman will search repositories in the order defined here
#   - local/custom mirrors can be added here or in separate files
#   - repositories listed first will take precedence when packages
#     have identical names, regardless of version number
#   - URLs will have $repo replaced by the name of the current repo
#   - URLs will have $arch replaced by the name of the architecture
#
# Repository entries are of the format:
#       [repo-name]
#       Server = ServerName
#       Include = IncludePath
#
# The header [repo-name] is crucial - it must be present and
# uncommented to enable the repo.
#

# The testing repositories are disabled by default. To enable, uncomment the
# repo name header and Include lines. You can add preferred servers immediately
# after the header, and they will be used before the default mirrors.

#[testing]
#Include = /etc/pacman.d/mirrorlist

[core]
Include = /etc/pacman.d/mirrorlist

[extra]
Include = /etc/pacman.d/mirrorlist

#[community-testing]
#Include = /etc/pacman.d/mirrorlist

#[community]
#Include = /etc/pacman.d/mirrorlist

# If you want to run 32 bit applications on your x86_64 system,
# enable the multilib repositories as required here.

#[multilib-testing]
#Include = /etc/pacman.d/mirrorlist

[multilib]
Include = /etc/pacman.d/mirrorlist

#[kernel-lts]
#Server = https://repo.m2x.dev/current/$repo/$arch
	
# An example of a custom package repository.  See the pacman manpage for
# tips on creating your own repositories.
#[custom]
#SigLevel = Optional TrustAll
#Server = file:///home/custompkgs

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

==> dkms install --no-depmod vboxhost/7.2.8_OSE -k 6.19.12-arch1-1
stat: cannot statx '/proc/1/root': Permesso negato
==> depmod 6.19.12-arch1-1

seems to come from dkms install…

stat -c %d:%i /; sudo stat -c %d:%i /proc/1/root/.

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

stat -c %d:%i /; sudo stat -c %d:%i /proc/1/root/.

stat -c %d:%i /; sudo stat -c %d:%i /proc/1/root/.
2049:2
stat: cannot statx '/proc/1/root/.': Permesso negato

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

You cannot

sudo /proc/1/root/.

? As root?

sudo  id
ls -l /proc/1

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

No, i can't

[root@dax-arch davide]# /proc/1/root/.
bash: /proc/1/root/.: Permesso negato
[root@dax-arch davide]# id
uid=0(root) gid=0(root) gruppi=0(root),1(bin),2(daemon),3(sys),4(adm),6(disk),10(wheel),19(log)
[root@dax-arch davide]# ls -l /proc/1
ls: impossibile leggere il collegamento simbolico '/proc/1/cwd': Permesso negato
ls: impossibile leggere il collegamento simbolico '/proc/1/root': Permesso negato
ls: impossibile leggere il collegamento simbolico '/proc/1/exe': Permesso negato
totale 0
-r--r--r--  1 root root   0 22 apr 15.04 arch_status
dr-xr-xr-x  2 root root   0 22 apr 15.04 attr
-rw-r--r--  1 root root   0 22 apr 15.04 autogroup
-r--------  1 root root   0 22 apr 15.04 auxv
-r--r--r--  1 root root   0 22 apr 14.15 cgroup
--w-------  1 root root   0 22 apr 15.04 clear_refs
-r--r--r--  1 root root   0 22 apr 15.04 cmdline
-rw-r--r--  1 root root   0 22 apr 15.04 comm
-rw-r--r--  1 root root   0 22 apr 15.04 coredump_filter
-r--r--r--  1 root root   0 22 apr 15.04 cpu_resctrl_groups
lrwxrwxrwx  1 root root   0 22 apr 15.04 cwd
-r--------  1 root root   0 22 apr 15.04 environ
lrwxrwxrwx  1 root root   0 22 apr 15.04 exe
dr-x------  2 root root 161 22 apr 15.04 fd
dr-xr-xr-x  2 root root   0 22 apr 15.04 fdinfo
-rw-r--r--  1 root root   0 22 apr 15.04 gid_map
-r--------  1 root root   0 22 apr 15.04 io
-r--------  1 root root   0 22 apr 15.04 ksm_merging_pages
-r--------  1 root root   0 22 apr 15.04 ksm_stat
-r--r--r--  1 root root   0 22 apr 15.04 limits
-rw-r--r--  1 root root   0 22 apr 15.04 loginuid
dr-x------  2 root root   0 22 apr 15.04 map_files
-r--r--r--  1 root root   0 22 apr 15.04 maps
-rw-------  1 root root   0 22 apr 15.04 mem
-r--r--r--  1 root root   0 22 apr 11.58 mountinfo
-r--r--r--  1 root root   0 22 apr 15.04 mounts
-r--------  1 root root   0 22 apr 15.04 mountstats
dr-xr-xr-x 38 root root   0 22 apr 15.04 net
dr-x--x--x  2 root root   0 22 apr 15.04 ns
-r--r--r--  1 root root   0 22 apr 15.04 numa_maps
-rw-r--r--  1 root root   0 22 apr 15.04 oom_adj
-r--r--r--  1 root root   0 22 apr 15.04 oom_score
-rw-r--r--  1 root root   0 22 apr 15.04 oom_score_adj
-r--------  1 root root   0 22 apr 15.04 pagemap
-r--------  1 root root   0 22 apr 15.04 personality
-rw-r--r--  1 root root   0 22 apr 15.04 projid_map
lrwxrwxrwx  1 root root   0 22 apr 14.08 root
-rw-r--r--  1 root root   0 22 apr 15.04 sched
-r--r--r--  1 root root   0 22 apr 15.04 schedstat
-r--r--r--  1 root root   0 22 apr 15.04 sessionid
-rw-r--r--  1 root root   0 22 apr 15.04 setgroups
-r--r--r--  1 root root   0 22 apr 15.04 smaps
-r--r--r--  1 root root   0 22 apr 15.04 smaps_rollup
-r--------  1 root root   0 22 apr 15.04 stack
-r--r--r--  1 root root   0 22 apr 15.04 stat
-r--r--r--  1 root root   0 22 apr 15.04 statm
-r--r--r--  1 root root   0 22 apr 15.04 status
-r--------  1 root root   0 22 apr 15.04 syscall
dr-xr-xr-x  3 root root   0 22 apr 15.04 task
-rw-r--r--  1 root root   0 22 apr 15.04 timens_offsets
-r--r--r--  1 root root   0 22 apr 15.04 timers
-rw-rw-rw-  1 root root   0 22 apr 15.04 timerslack_ns
-rw-r--r--  1 root root   0 22 apr 15.04 uid_map
-r--r--r--  1 root root   0 22 apr 15.04 wchan

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

mount | grep proc

Then reboot, does the problem remain?

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

mount | grep proc
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=42,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=1901)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)

And after a reboot

[root@dax-arch davide]# /proc/1/root/.
bash: /proc/1/root/.: Permesso negato

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Please post your complete system journal for the boot:

sudo journalctl -b | curl -s -H "Accept: application/json, */*" --upload-file - 'https://paste.c-net.org/'

Something's fishy here - why can't root access /proc/1/root ?

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

Here
Thanks again

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

The most red flag is https://wiki.archlinux.org/title/SLiM
Try to only boot the multi-user.target (2nd link below) and check access to /proc/1/root/ there (you will require root permissions for sure, but should not run into issues then)

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

I type 'e' when grub entries appears and i add

systemd.unit=multi-user.target

ctrl+x and boot in graphical mode.
I get root privileges but if i type

 /proc/1/root/.
bash: /proc/1/root/.: È una directory

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

bash: /proc/1/root/.: È una directory

still

stat /proc/1/root/.

though the mere fact that bash can tell that this is a directory smells like slim is actually the cause.
Do you actually need a DM? If so, try maybe lightdm.

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

With slim running

stat /proc/1/root/.
stat: cannot statx '/proc/1/root/.': Permesso negato

and without

stat /proc/1/root/.
  File: /proc/1/root/.
  Dim.: 4096      	Blocchi: 8          Blocco di IO: 4096   directory
Device: 8,1	Inode: 2           Links: 18
Accesso: (0755/drwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Accesso  : 2026-04-22 11:59:22.644852913 +0200
Modifica : 2026-04-21 11:12:16.297267618 +0200
Cambio   : 2026-04-21 11:12:16.297267618 +0200
Creazione: 2016-08-19 14:45:14.000000000 +0200

Do you actually need a DM? If so, try maybe lightdm.

Probably not, i use mate and i will investigate how to start it.

seth

Member

From: Won't reply 2 private help req

Registered: 2012-09-03

Posts: 74,697

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

https://wiki.archlinux.org/title/MATE#Starting_MATE
If you're going for xinitrc, see the last link below (2nd blue note about what to include at least)

Please always remember to mark resolved threads by editing your initial posts subject - so others will know that there's no task left, but maybe a solution to find.
Thanks.

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dax79

Member

Registered: 2021-12-28

Posts: 18

Re: [SOLVED]Failed to check for chroot() environment: Permission denied

https://wiki.archlinux.org/title/MATE#Starting_MATE
If you're going for xinitrc, see the last link below (2nd blue note about what to include at least)

Please always remember to mark resolved threads by editing your initial posts subject - so others will know that there's no task left, but maybe a solution to find.
Thanks.

Thanks, i will look.
I try to disable slim, startx and the error when i run 'pacman -Syu' disappear.