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#751 2013-06-29 22:09:00

cfr
Member
From: Cymru
Registered: 2011-11-27
Posts: 5,661

Re: filesystem Update Error /bin exists in filesystem

Please use quote tags like

this

.
And

code tags

where appropriate.

I cannot tell from your post what you are quoting and what you are not quoting so I have no idea what you did. However, it sounds as if you forgot to update bash.


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#752 2013-06-29 22:20:35

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

vivithemage wrote:

For my system /bin contains sh and bash, /sbin doesn't even exist and /usr/sbin is empty hmm

I ended up moving /bin to /bin-old then creating symlinks to /usr/bin

All seems fine now and boots correctly but the networking and perhaps some other things are not functioning correctly so there's a new barrel of fun to get in to tongue

You forgot the second command of step 5, it would have moved /bin/bash and /bin/sh for you.

Last edited by Scimmia (2013-06-29 22:21:06)

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#753 2013-06-29 22:51:32

jasonwryan
Forum & Wiki Admin
From: .nz
Registered: 2009-05-09
Posts: 18,109
Website

Re: filesystem Update Error /bin exists in filesystem

Merging with the stickied thread...


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#754 2013-06-30 20:51:40

akanski
Member
Registered: 2011-09-30
Posts: 31

Re: filesystem Update Error /bin exists in filesystem

@bananagranola,

Moving some binaries to /usr/bin is not "something stupid", don't be so uncharitable about yourself (#745). Anyway, you'll be able to remove non-official packages with files in /bin and /sbin through the new symlinks in your filesystem, so there's no need to be so dramatic about that unless you take a very long time to put everything in order and backward compatibility is deprecated. Moreover, although that's definitely not the case, why have symbolic links for /bin and /sbin if they are useless?

Even if by any chance your memory fails to undo that bad idea of putting your own scripts in /usr/bin, you'll be able to fix any mishmash in that directory by means of commands such as find, pacman, sort, comm, etc. For example, I use something like this stuff to get rid of orphan and disused files:

find /usr -not -name *.cache -not -name *.pacnew -not -name fonts.* -not -path '/usr/lib/locale/*' -not -path '/usr/share/info/dir' -not -path '/usr/share/mime/*' -not -path '/usr/local/*/*' | sort > /tmp/current-fs_usr-files.txt
pacman -Qql | sed -e 's/\/*$//' | sort -u | grep '/usr' > /tmp/pacman-list_usr-files.txt
comm -32 /tmp/current-fs_usr-files.txt /tmp/pacman-list_usr-files.txt | less

However, if you want to do the same, make sure you don't delete files created by existing programs and don't forget to make a backup as precautionary measure:

comm -32 /tmp/current-fs_usr-files.txt /tmp/pacman-list_usr-files.txt > /tmp/possible_orphan_usr-files.txt
tar -cJvf /root/backup_orphan_usr-files.tar.xz --files-from /tmp/possible_orphan_usr-files.txt

Incidentally, you can edit the previous output, providing you certainly know what files don't have to be backed up.

To round off I'd like to say that you can also put your own scripts in /usr/local/bin so that they are available for everybody. In addition, you can add "~/bin" to your own path in the individual per-interactive-shell startup file ~/.bashrc thus (in case you use GNU Bourne-Again SHell):

if [ -d ~/bin ]; then
    PATH=~/bin:"${PATH}"
    export PATH
fi

___

N.B. Considering that /var is for variable data, using the above commands in that directory is very risky and unwise (your system might be unusable if you do something wrong). Likewise, be careful with /etc as well as another critical directories, moreover, don't touch /boot since there's no reason to do that either.

Last edited by akanski (2013-07-02 19:40:47)

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#755 2013-07-01 15:27:46

stabu
Member
Registered: 2010-01-14
Posts: 19

Re: filesystem Update Error /bin exists in filesystem

Hi,

Any help on my problem appreciated.

The following output is occurring. It seems to be multilib related. Can get anythng from journalctl onit
root@rfmp: # pacman -Su
:: Starting full system upgrade...
:: Replace grub-bios with core/grub? [Y/n] n
:: Replace grub-common with core/grub? [Y/n] n
:: Replace grub-efi-x86_64 with core/grub? [Y/n] n
resolving dependencies...
warning: dependency cycle detected:
warning: lib32-gcc-libs will be installed before its gcc-libs-multilib dependency
looking for inter-conflicts...

Packages (187):
....
Proceed with installation? [Y/n] Y
(187/187) checking keys in keyring                                    [#############################################################################] 100%
(187/187) checking package integrity                                  [#############################################################################] 100%
(187/187) loading package files                                       [#############################################################################] 100%
(187/187) checking for file conflicts                                 [#############################################################################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /bin exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/sbin exists in filesystem
Errors occurred, no packages were upgraded.


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#756 2013-07-01 15:28:27

karol
Archivist
Registered: 2009-05-06
Posts: 25,423

Re: filesystem Update Error /bin exists in filesystem

Have you read the news from https://www.archlinux.org/ ?

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#757 2013-07-01 19:46:45

jasonwryan
Forum & Wiki Admin
From: .nz
Registered: 2009-05-09
Posts: 18,109
Website

Re: filesystem Update Error /bin exists in filesystem

Merging with the stickied thread...


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#758 2013-07-02 07:46:24

stabu
Member
Registered: 2010-01-14
Posts: 19

Re: filesystem Update Error /bin exists in filesystem

Hi ....

First, apologies, I didn't read the news. This change happened while i attend a training course, soIwasn't paying100% attention. Second, thanks for the replies.

The steps in the news item assume I know how to fix a package and that I'm happy doing stuff like "cp /usr/sbin/* /usr/bin".

I'm neither unfortunately. So I'll have to wait until I have a full weekend to see the full implications,and avoid leading to a unbootable system.


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#759 2013-07-02 19:00:21

cfr
Member
From: Cymru
Registered: 2011-11-27
Posts: 5,661

Re: filesystem Update Error /bin exists in filesystem

stabu wrote:

Hi ....

First, apologies, I didn't read the news. This change happened while i attend a training course, soIwasn't paying100% attention. Second, thanks for the replies.

The steps in the news item assume I know how to fix a package

Read the thread this is merged to. (Not the whole thing - the same information is essentially repeated over and over so you only need read one chunk.

and that I'm happy doing stuff like "cp /usr/sbin/* /usr/bin".

No. Do not do this. Not being happy doing this is a good thing. Doing it will break stuff.


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#760 2013-07-04 02:56:58

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

So i was about to update today and noticed the news on the homepage.  The problem is that I'm not exactly sure how to go about fixing these issues.  The first command yields this result:

$ pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
grub-common 2.00-1

I am not quite sure where grub-common is or what I need to do with it.  I assume I simply need to move it to /usr/bin but I'm not quite sure.  The next command yields this for the catalyst repo:

$ paclist catalyst | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
apache /usr/sbin/
apache /usr/sbin/ab
apache /usr/sbin/apachectl
apache /usr/sbin/apxs
apache /usr/sbin/checkgid
apache /usr/sbin/dbmmanage
apache /usr/sbin/envvars
apache /usr/sbin/envvars-std
apache /usr/sbin/htcacheclean
apache /usr/sbin/htdbm
apache /usr/sbin/htdigest
apache /usr/sbin/htpasswd
apache /usr/sbin/httpd
apache /usr/sbin/httpd.itk
apache /usr/sbin/httpd.worker
apache /usr/sbin/httxt2dbm
apache /usr/sbin/logresolve
apache /usr/sbin/rotatelogs
apache /usr/sbin/suexec
avahi /usr/sbin/
avahi /usr/sbin/avahi-autoipd
avahi /usr/sbin/avahi-daemon
avahi /usr/sbin/avahi-dnsconfd
bash /bin/
bash /bin/bash
bash /bin/sh
bluez /usr/sbin/
bluez /usr/sbin/bccmd
bluez /usr/sbin/bluetoothd
bluez /usr/sbin/hciattach
bluez /usr/sbin/hciconfig
catalyst-utils /usr/sbin/
catalyst-utils /usr/sbin/amdnotifyui
catalyst-utils /usr/sbin/atieventsd
catalyst-utils /usr/sbin/atigetsysteminfo.sh
cdrkit /usr/sbin/
cdrkit /usr/sbin/netscsid
cifs-utils /usr/sbin/
cifs-utils /usr/sbin/cifs.idmap
cifs-utils /usr/sbin/cifs.upcall
coreutils /bin/
coreutils /bin/cat
coreutils /bin/chgrp
coreutils /bin/chmod
coreutils /bin/chown
coreutils /bin/cp
coreutils /bin/date
coreutils /bin/dd
coreutils /bin/df
coreutils /bin/echo
coreutils /bin/false
coreutils /bin/ln
coreutils /bin/ls
coreutils /bin/mkdir
coreutils /bin/mknod
coreutils /bin/mv
coreutils /bin/pwd
coreutils /bin/rm
coreutils /bin/rmdir
coreutils /bin/stty
coreutils /bin/sync
coreutils /bin/true
coreutils /bin/uname
cracklib /usr/sbin/
cracklib /usr/sbin/cracklib-check
cracklib /usr/sbin/cracklib-format
cracklib /usr/sbin/cracklib-packer
cracklib /usr/sbin/cracklib-unpacker
cracklib /usr/sbin/create-cracklib-dict
cronie /usr/sbin/
cronie /usr/sbin/anacron
cronie /usr/sbin/crond
cryptsetup /usr/sbin/
cryptsetup /usr/sbin/cryptsetup
cryptsetup /usr/sbin/cryptsetup-reencrypt
cryptsetup /usr/sbin/veritysetup
device-mapper /usr/sbin/
device-mapper /usr/sbin/dmeventd
device-mapper /usr/sbin/dmsetup
dhclient /sbin/
dhclient /sbin/dhclient-script
dhclient /usr/sbin/
dhclient /usr/sbin/dhclient
dhcpcd /sbin/
dhcpcd /sbin/dhcpcd
dhcpcd /usr/sbin/
dhcpcd /usr/sbin/dhcpcd
e2fsprogs /sbin/
e2fsprogs /sbin/badblocks
e2fsprogs /sbin/debugfs
e2fsprogs /sbin/dumpe2fs
e2fsprogs /sbin/e2fsck
e2fsprogs /sbin/e2image
e2fsprogs /sbin/e2label
e2fsprogs /sbin/e2undo
e2fsprogs /sbin/fsck.ext2
e2fsprogs /sbin/fsck.ext3
e2fsprogs /sbin/fsck.ext4
e2fsprogs /sbin/fsck.ext4dev
e2fsprogs /sbin/logsave
e2fsprogs /sbin/mke2fs
e2fsprogs /sbin/mkfs.ext2
e2fsprogs /sbin/mkfs.ext3
e2fsprogs /sbin/mkfs.ext4
e2fsprogs /sbin/mkfs.ext4dev
e2fsprogs /sbin/resize2fs
e2fsprogs /sbin/tune2fs
e2fsprogs /usr/sbin/
e2fsprogs /usr/sbin/e2freefrag
e2fsprogs /usr/sbin/e4defrag
e2fsprogs /usr/sbin/filefrag
e2fsprogs /usr/sbin/mklost+found
filesystem /usr/sbin/
fuse /bin/
fuse /bin/fusermount
fuse /bin/ulockmgr_server
fuse /sbin/
fuse /sbin/mount.fuse
gawk /bin/
gawk /bin/awk
gawk /bin/gawk
gconf /usr/sbin/
gconf /usr/sbin/gconfpkg
gdm /usr/sbin/
gdm /usr/sbin/gdm
glibc /sbin/
glibc /sbin/ldconfig
glibc /sbin/sln
glibc /usr/sbin/
glibc /usr/sbin/iconvconfig
glibc /usr/sbin/nscd
glibc /usr/sbin/zdump
glibc /usr/sbin/zic
gpm /usr/sbin/
gpm /usr/sbin/gpm
grub-common /usr/sbin/
grub-common /usr/sbin/grub-bios-setup
grub-common /usr/sbin/grub-install
grub-common /usr/sbin/grub-mkconfig
grub-common /usr/sbin/grub-mknetdir
grub-common /usr/sbin/grub-ofpathname
grub-common /usr/sbin/grub-probe
grub-common /usr/sbin/grub-reboot
grub-common /usr/sbin/grub-set-default
grub-common /usr/sbin/grub-sparc64-setup
icu /usr/sbin/
icu /usr/sbin/genccode
icu /usr/sbin/gencmn
icu /usr/sbin/gennorm2
icu /usr/sbin/gensprep
icu /usr/sbin/icupkg
inetutils /bin/
inetutils /bin/dnsdomainname
inetutils /bin/hostname
iproute2 /sbin/
iproute2 /sbin/ip
iproute2 /usr/sbin/
iproute2 /usr/sbin/arpd
iproute2 /usr/sbin/bridge
iproute2 /usr/sbin/ctstat
iproute2 /usr/sbin/genl
iproute2 /usr/sbin/ifcfg
iproute2 /usr/sbin/ifstat
iproute2 /usr/sbin/ip
iproute2 /usr/sbin/lnstat
iproute2 /usr/sbin/nstat
iproute2 /usr/sbin/routef
iproute2 /usr/sbin/routel
iproute2 /usr/sbin/rtacct
iproute2 /usr/sbin/rtmon
iproute2 /usr/sbin/rtpr
iproute2 /usr/sbin/rtstat
iproute2 /usr/sbin/ss
iproute2 /usr/sbin/tc
iptables /usr/sbin/
iptables /usr/sbin/ip6tables
iptables /usr/sbin/ip6tables-restore
iptables /usr/sbin/ip6tables-save
iptables /usr/sbin/iptables
iptables /usr/sbin/iptables-restore
iptables /usr/sbin/iptables-save
iptables /usr/sbin/xtables-multi
jfsutils /sbin/
jfsutils /sbin/fsck.jfs
jfsutils /sbin/jfs_debugfs
jfsutils /sbin/jfs_fsck
jfsutils /sbin/jfs_fscklog
jfsutils /sbin/jfs_logdump
jfsutils /sbin/jfs_mkfs
jfsutils /sbin/jfs_tune
jfsutils /sbin/mkfs.jfs
kmod /sbin/
kmod /sbin/depmod
kmod /sbin/modprobe
libatasmart /usr/sbin/
libatasmart /usr/sbin/skdump
libatasmart /usr/sbin/sktest
libbonobo /usr/sbin/
libbonobo /usr/sbin/bonobo-activation-sysconf
libsasl /usr/sbin/
libsasl /usr/sbin/pluginviewer
libsasl /usr/sbin/sasldblistusers2
libsasl /usr/sbin/saslpasswd2
lirc-utils /usr/sbin/
lirc-utils /usr/sbin/lircd
lirc-utils /usr/sbin/lircmd
lsof /usr/sbin/
lsof /usr/sbin/lsof
lvm2 /usr/sbin/
lvm2 /usr/sbin/blkdeactivate
lvm2 /usr/sbin/fsadm
lvm2 /usr/sbin/lvchange
lvm2 /usr/sbin/lvconvert
lvm2 /usr/sbin/lvcreate
lvm2 /usr/sbin/lvdisplay
lvm2 /usr/sbin/lvextend
lvm2 /usr/sbin/lvm
lvm2 /usr/sbin/lvmchange
lvm2 /usr/sbin/lvmconf
lvm2 /usr/sbin/lvmdiskscan
lvm2 /usr/sbin/lvmdump
lvm2 /usr/sbin/lvmetad
lvm2 /usr/sbin/lvmsadc
lvm2 /usr/sbin/lvmsar
lvm2 /usr/sbin/lvreduce
lvm2 /usr/sbin/lvremove
lvm2 /usr/sbin/lvrename
lvm2 /usr/sbin/lvresize
lvm2 /usr/sbin/lvs
lvm2 /usr/sbin/lvscan
lvm2 /usr/sbin/pvchange
lvm2 /usr/sbin/pvck
lvm2 /usr/sbin/pvcreate
lvm2 /usr/sbin/pvdisplay
lvm2 /usr/sbin/pvmove
lvm2 /usr/sbin/pvremove
lvm2 /usr/sbin/pvresize
lvm2 /usr/sbin/pvs
lvm2 /usr/sbin/pvscan
lvm2 /usr/sbin/vgcfgbackup
lvm2 /usr/sbin/vgcfgrestore
lvm2 /usr/sbin/vgchange
lvm2 /usr/sbin/vgck
lvm2 /usr/sbin/vgconvert
lvm2 /usr/sbin/vgcreate
lvm2 /usr/sbin/vgdisplay
lvm2 /usr/sbin/vgexport
lvm2 /usr/sbin/vgextend
lvm2 /usr/sbin/vgimport
lvm2 /usr/sbin/vgimportclone
lvm2 /usr/sbin/vgmerge
lvm2 /usr/sbin/vgmknodes
lvm2 /usr/sbin/vgreduce
lvm2 /usr/sbin/vgremove
lvm2 /usr/sbin/vgrename
lvm2 /usr/sbin/vgs
lvm2 /usr/sbin/vgscan
lvm2 /usr/sbin/vgsplit
man-db /usr/sbin/
man-db /usr/sbin/accessdb
mdadm /sbin/
mdadm /sbin/mdadm
mdadm /sbin/mdassemble
mdadm /sbin/mdmon
modemmanager /usr/sbin/
modemmanager /usr/sbin/ModemManager
net-tools /bin/
net-tools /bin/netstat
net-tools /sbin/
net-tools /sbin/arp
net-tools /sbin/ifconfig
net-tools /sbin/ipmaddr
net-tools /sbin/iptunnel
net-tools /sbin/mii-tool
net-tools /sbin/nameif
net-tools /sbin/plipconfig
net-tools /sbin/rarp
net-tools /sbin/route
net-tools /sbin/slattach
networkmanager /usr/sbin/
networkmanager /usr/sbin/NetworkManager
openssh /usr/sbin/
openssh /usr/sbin/sshd
pam /sbin/
pam /sbin/mkhomedir_helper
pam /sbin/pam_tally
pam /sbin/pam_tally2
pam /sbin/pam_timestamp_check
pam /sbin/unix_chkpwd
pam /sbin/unix_update
parted /usr/sbin/
parted /usr/sbin/parted
parted /usr/sbin/partprobe
pciutils /usr/sbin/
pciutils /usr/sbin/lspci
pciutils /usr/sbin/setpci
pm-utils /usr/sbin/
pm-utils /usr/sbin/pm-hibernate
pm-utils /usr/sbin/pm-powersave
pm-utils /usr/sbin/pm-suspend
pm-utils /usr/sbin/pm-suspend-hybrid
ppp /usr/sbin/
ppp /usr/sbin/chat
ppp /usr/sbin/plog
ppp /usr/sbin/pppd
ppp /usr/sbin/pppdump
ppp /usr/sbin/pppoe-discovery
ppp /usr/sbin/pppstats
procps-ng /bin/
procps-ng /bin/ps
procps-ng /sbin/
procps-ng /sbin/sysctl
reiserfsprogs /sbin/
reiserfsprogs /sbin/debugreiserfs
reiserfsprogs /sbin/fsck.reiserfs
reiserfsprogs /sbin/mkfs.reiserfs
reiserfsprogs /sbin/mkreiserfs
reiserfsprogs /sbin/reiserfsck
reiserfsprogs /sbin/reiserfstune
reiserfsprogs /sbin/resize_reiserfs
rtmpdump /usr/sbin/
rtmpdump /usr/sbin/rtmpgw
rtmpdump /usr/sbin/rtmpsrv
rtmpdump /usr/sbin/rtmpsuck
sed /bin/
sed /bin/sed
shadow /bin/
shadow /bin/groups
shadow /sbin/
shadow /sbin/nologin
shadow /usr/sbin/
shadow /usr/sbin/chgpasswd
shadow /usr/sbin/chpasswd
shadow /usr/sbin/groupadd
shadow /usr/sbin/groupdel
shadow /usr/sbin/groupmems
shadow /usr/sbin/groupmod
shadow /usr/sbin/grpck
shadow /usr/sbin/grpconv
shadow /usr/sbin/grpunconv
shadow /usr/sbin/newusers
shadow /usr/sbin/pwck
shadow /usr/sbin/pwconv
shadow /usr/sbin/pwunconv
shadow /usr/sbin/useradd
shadow /usr/sbin/userdel
shadow /usr/sbin/usermod
systemd /sbin/
systemd /sbin/udevadm
systemd-sysvcompat /sbin/
systemd-sysvcompat /sbin/halt
systemd-sysvcompat /sbin/init
systemd-sysvcompat /sbin/poweroff
systemd-sysvcompat /sbin/reboot
systemd-sysvcompat /sbin/runlevel
systemd-sysvcompat /sbin/shutdown
systemd-sysvcompat /sbin/telinit
sysvinit-tools /bin/
sysvinit-tools /bin/pidof
sysvinit-tools /sbin/
sysvinit-tools /sbin/bootlogd
sysvinit-tools /sbin/fstab-decode
sysvinit-tools /sbin/killall5
tar /bin/
tar /bin/tar
tcpdump /usr/sbin/
tcpdump /usr/sbin/tcpdump
udisks2 /usr/sbin/
udisks2 /usr/sbin/umount.udisks2
usbmuxd /usr/sbin/
usbmuxd /usr/sbin/usbmuxd
util-linux /bin/
util-linux /bin/dmesg
util-linux /bin/findmnt
util-linux /bin/kill
util-linux /bin/login
util-linux /bin/lsblk
util-linux /bin/more
util-linux /bin/mount
util-linux /bin/mountpoint
util-linux /bin/su
util-linux /bin/umount
util-linux /bin/wdctl
util-linux /sbin/
util-linux /sbin/agetty
util-linux /sbin/blkdiscard
util-linux /sbin/blkid
util-linux /sbin/blockdev
util-linux /sbin/cfdisk
util-linux /sbin/chcpu
util-linux /sbin/ctrlaltdel
util-linux /sbin/fdisk
util-linux /sbin/findfs
util-linux /sbin/fsck
util-linux /sbin/fsck.cramfs
util-linux /sbin/fsck.minix
util-linux /sbin/fsfreeze
util-linux /sbin/fstrim
util-linux /sbin/hwclock
util-linux /sbin/losetup
util-linux /sbin/mkfs
util-linux /sbin/mkfs.bfs
util-linux /sbin/mkfs.cramfs
util-linux /sbin/mkfs.minix
util-linux /sbin/mkswap
util-linux /sbin/pivot_root
util-linux /sbin/raw
util-linux /sbin/runuser
util-linux /sbin/sfdisk
util-linux /sbin/sulogin
util-linux /sbin/swaplabel
util-linux /sbin/swapoff
util-linux /sbin/swapon
util-linux /sbin/switch_root
util-linux /sbin/wipefs
util-linux /usr/sbin/
util-linux /usr/sbin/addpart
util-linux /usr/sbin/delpart
util-linux /usr/sbin/fdformat
util-linux /usr/sbin/ldattach
util-linux /usr/sbin/partx
util-linux /usr/sbin/readprofile
util-linux /usr/sbin/resizepart
util-linux /usr/sbin/rtcwake
util-linux /usr/sbin/uuidd
util-linux /usr/sbin/vigr
util-linux /usr/sbin/vipw
v4l-utils /usr/sbin/
v4l-utils /usr/sbin/v4l2-dbg
wireless_tools /usr/sbin/
wireless_tools /usr/sbin/ifrename
wireless_tools /usr/sbin/iwconfig
wireless_tools /usr/sbin/iwevent
wireless_tools /usr/sbin/iwgetid
wireless_tools /usr/sbin/iwlist
wireless_tools /usr/sbin/iwpriv
wireless_tools /usr/sbin/iwspy
wpa_supplicant /usr/sbin/
wpa_supplicant /usr/sbin/wpa_cli
wpa_supplicant /usr/sbin/wpa_passphrase
wpa_supplicant /usr/sbin/wpa_supplicant
xfsprogs /sbin/
xfsprogs /sbin/fsck.xfs
xfsprogs /sbin/mkfs.xfs
xfsprogs /sbin/xfs_repair
xfsprogs /usr/sbin/
xfsprogs /usr/sbin/xfs_admin
xfsprogs /usr/sbin/xfs_bmap
xfsprogs /usr/sbin/xfs_check
xfsprogs /usr/sbin/xfs_copy
xfsprogs /usr/sbin/xfs_db
xfsprogs /usr/sbin/xfs_estimate
xfsprogs /usr/sbin/xfs_freeze
xfsprogs /usr/sbin/xfs_fsr
xfsprogs /usr/sbin/xfs_growfs
xfsprogs /usr/sbin/xfs_info
xfsprogs /usr/sbin/xfs_io
xfsprogs /usr/sbin/xfs_logprint
xfsprogs /usr/sbin/xfs_mdrestore
xfsprogs /usr/sbin/xfs_metadump
xfsprogs /usr/sbin/xfs_mkfile
xfsprogs /usr/sbin/xfs_ncheck
xfsprogs /usr/sbin/xfs_quota
xfsprogs /usr/sbin/xfs_rtcp
xinetd /usr/sbin/
xinetd /usr/sbin/itox
xinetd /usr/sbin/xconv.pl
xinetd /usr/sbin/xinetd
zvbi /usr/sbin/
zvbi /usr/sbin/zvbid

Does this mean that I need to move all of those things to /usr/bin?  I figured maybe I could just do something like this:

#!/bin/bash

for file in $(paclist catalyst | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/' | awk '{print $2}' )
do
     mv $file /usr/bin
done

This obviously won't work because I'll end up throwing /sbin and /bin in /usr/bin as well as a bunch of things that I probably don't need to be moving around like /usr/sbin/lspci and /usr/sbin/parted for example.  I obviously am trying to go about this the wrong way and could use a little help.

Offline

#761 2013-07-04 03:06:14

cfr
Member
From: Cymru
Registered: 2011-11-27
Posts: 5,661

Re: filesystem Update Error /bin exists in filesystem

Don't move them manually. Update the packages.

Please search before posting. There is an extremely long stickied thread covering every permutation at this point. Read a section of it and follow the advice there. (You only need a section because it loops.)

I expect this will merge with that thread shortly...


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Offline

#762 2013-07-04 03:10:00

jasonwryan
Forum & Wiki Admin
From: .nz
Registered: 2009-05-09
Posts: 18,109
Website

Re: filesystem Update Error /bin exists in filesystem

cfr wrote:

I expect this will merge with that thread shortly...


How prescient of you.


Arch + dwm   •   Mercurial repos  •   Github

Registered Linux User #482438

Offline

#763 2013-07-04 04:03:50

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

instantaphex wrote:

So i was about to update today and noticed the news on the homepage.  The problem is that I'm not exactly sure how to go about fixing these issues.  The first command yields this result:

$ pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
grub-common 2.00-1

I am not quite sure where grub-common is or what I need to do with it.  I assume I simply need to move it to /usr/bin but I'm not quite sure.

grub-common will be replaced by grub, so don't worry about it.

instantaphex wrote:

The next command yields this for the catalyst repo:

$ paclist catalyst | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
apache /usr/sbin/
apache /usr/sbin/ab
apache /usr/sbin/apachectl
apache /usr/sbin/apxs
apache /usr/sbin/checkgid
apache /usr/sbin/dbmmanage
apache /usr/sbin/envvars
apache /usr/sbin/envvars-std
apache /usr/sbin/htcacheclean
apache /usr/sbin/htdbm
apache /usr/sbin/htdigest
apache /usr/sbin/htpasswd
apache /usr/sbin/httpd
apache /usr/sbin/httpd.itk
apache /usr/sbin/httpd.worker
apache /usr/sbin/httxt2dbm
apache /usr/sbin/logresolve
apache /usr/sbin/rotatelogs
apache /usr/sbin/suexec
avahi /usr/sbin/
avahi /usr/sbin/avahi-autoipd
avahi /usr/sbin/avahi-daemon
avahi /usr/sbin/avahi-dnsconfd
bash /bin/
bash /bin/bash
bash /bin/sh
bluez /usr/sbin/
bluez /usr/sbin/bccmd
bluez /usr/sbin/bluetoothd
bluez /usr/sbin/hciattach
bluez /usr/sbin/hciconfig
catalyst-utils /usr/sbin/
catalyst-utils /usr/sbin/amdnotifyui
catalyst-utils /usr/sbin/atieventsd
catalyst-utils /usr/sbin/atigetsysteminfo.sh
cdrkit /usr/sbin/
cdrkit /usr/sbin/netscsid
cifs-utils /usr/sbin/
cifs-utils /usr/sbin/cifs.idmap
cifs-utils /usr/sbin/cifs.upcall
coreutils /bin/
coreutils /bin/cat
coreutils /bin/chgrp
coreutils /bin/chmod
coreutils /bin/chown
coreutils /bin/cp
coreutils /bin/date
coreutils /bin/dd
coreutils /bin/df
coreutils /bin/echo
coreutils /bin/false
coreutils /bin/ln
coreutils /bin/ls
coreutils /bin/mkdir
coreutils /bin/mknod
coreutils /bin/mv
coreutils /bin/pwd
coreutils /bin/rm
coreutils /bin/rmdir
coreutils /bin/stty
coreutils /bin/sync
coreutils /bin/true
coreutils /bin/uname
cracklib /usr/sbin/
cracklib /usr/sbin/cracklib-check
cracklib /usr/sbin/cracklib-format
cracklib /usr/sbin/cracklib-packer
cracklib /usr/sbin/cracklib-unpacker
cracklib /usr/sbin/create-cracklib-dict
cronie /usr/sbin/
cronie /usr/sbin/anacron
cronie /usr/sbin/crond
cryptsetup /usr/sbin/
cryptsetup /usr/sbin/cryptsetup
cryptsetup /usr/sbin/cryptsetup-reencrypt
cryptsetup /usr/sbin/veritysetup
device-mapper /usr/sbin/
device-mapper /usr/sbin/dmeventd
device-mapper /usr/sbin/dmsetup
dhclient /sbin/
dhclient /sbin/dhclient-script
dhclient /usr/sbin/
dhclient /usr/sbin/dhclient
dhcpcd /sbin/
dhcpcd /sbin/dhcpcd
dhcpcd /usr/sbin/
dhcpcd /usr/sbin/dhcpcd
e2fsprogs /sbin/
e2fsprogs /sbin/badblocks
e2fsprogs /sbin/debugfs
e2fsprogs /sbin/dumpe2fs
e2fsprogs /sbin/e2fsck
e2fsprogs /sbin/e2image
e2fsprogs /sbin/e2label
e2fsprogs /sbin/e2undo
e2fsprogs /sbin/fsck.ext2
e2fsprogs /sbin/fsck.ext3
e2fsprogs /sbin/fsck.ext4
e2fsprogs /sbin/fsck.ext4dev
e2fsprogs /sbin/logsave
e2fsprogs /sbin/mke2fs
e2fsprogs /sbin/mkfs.ext2
e2fsprogs /sbin/mkfs.ext3
e2fsprogs /sbin/mkfs.ext4
e2fsprogs /sbin/mkfs.ext4dev
e2fsprogs /sbin/resize2fs
e2fsprogs /sbin/tune2fs
e2fsprogs /usr/sbin/
e2fsprogs /usr/sbin/e2freefrag
e2fsprogs /usr/sbin/e4defrag
e2fsprogs /usr/sbin/filefrag
e2fsprogs /usr/sbin/mklost+found
filesystem /usr/sbin/
fuse /bin/
fuse /bin/fusermount
fuse /bin/ulockmgr_server
fuse /sbin/
fuse /sbin/mount.fuse
gawk /bin/
gawk /bin/awk
gawk /bin/gawk
gconf /usr/sbin/
gconf /usr/sbin/gconfpkg
gdm /usr/sbin/
gdm /usr/sbin/gdm
glibc /sbin/
glibc /sbin/ldconfig
glibc /sbin/sln
glibc /usr/sbin/
glibc /usr/sbin/iconvconfig
glibc /usr/sbin/nscd
glibc /usr/sbin/zdump
glibc /usr/sbin/zic
gpm /usr/sbin/
gpm /usr/sbin/gpm
grub-common /usr/sbin/
grub-common /usr/sbin/grub-bios-setup
grub-common /usr/sbin/grub-install
grub-common /usr/sbin/grub-mkconfig
grub-common /usr/sbin/grub-mknetdir
grub-common /usr/sbin/grub-ofpathname
grub-common /usr/sbin/grub-probe
grub-common /usr/sbin/grub-reboot
grub-common /usr/sbin/grub-set-default
grub-common /usr/sbin/grub-sparc64-setup
icu /usr/sbin/
icu /usr/sbin/genccode
icu /usr/sbin/gencmn
icu /usr/sbin/gennorm2
icu /usr/sbin/gensprep
icu /usr/sbin/icupkg
inetutils /bin/
inetutils /bin/dnsdomainname
inetutils /bin/hostname
iproute2 /sbin/
iproute2 /sbin/ip
iproute2 /usr/sbin/
iproute2 /usr/sbin/arpd
iproute2 /usr/sbin/bridge
iproute2 /usr/sbin/ctstat
iproute2 /usr/sbin/genl
iproute2 /usr/sbin/ifcfg
iproute2 /usr/sbin/ifstat
iproute2 /usr/sbin/ip
iproute2 /usr/sbin/lnstat
iproute2 /usr/sbin/nstat
iproute2 /usr/sbin/routef
iproute2 /usr/sbin/routel
iproute2 /usr/sbin/rtacct
iproute2 /usr/sbin/rtmon
iproute2 /usr/sbin/rtpr
iproute2 /usr/sbin/rtstat
iproute2 /usr/sbin/ss
iproute2 /usr/sbin/tc
iptables /usr/sbin/
iptables /usr/sbin/ip6tables
iptables /usr/sbin/ip6tables-restore
iptables /usr/sbin/ip6tables-save
iptables /usr/sbin/iptables
iptables /usr/sbin/iptables-restore
iptables /usr/sbin/iptables-save
iptables /usr/sbin/xtables-multi
jfsutils /sbin/
jfsutils /sbin/fsck.jfs
jfsutils /sbin/jfs_debugfs
jfsutils /sbin/jfs_fsck
jfsutils /sbin/jfs_fscklog
jfsutils /sbin/jfs_logdump
jfsutils /sbin/jfs_mkfs
jfsutils /sbin/jfs_tune
jfsutils /sbin/mkfs.jfs
kmod /sbin/
kmod /sbin/depmod
kmod /sbin/modprobe
libatasmart /usr/sbin/
libatasmart /usr/sbin/skdump
libatasmart /usr/sbin/sktest
libbonobo /usr/sbin/
libbonobo /usr/sbin/bonobo-activation-sysconf
libsasl /usr/sbin/
libsasl /usr/sbin/pluginviewer
libsasl /usr/sbin/sasldblistusers2
libsasl /usr/sbin/saslpasswd2
lirc-utils /usr/sbin/
lirc-utils /usr/sbin/lircd
lirc-utils /usr/sbin/lircmd
lsof /usr/sbin/
lsof /usr/sbin/lsof
lvm2 /usr/sbin/
lvm2 /usr/sbin/blkdeactivate
lvm2 /usr/sbin/fsadm
lvm2 /usr/sbin/lvchange
lvm2 /usr/sbin/lvconvert
lvm2 /usr/sbin/lvcreate
lvm2 /usr/sbin/lvdisplay
lvm2 /usr/sbin/lvextend
lvm2 /usr/sbin/lvm
lvm2 /usr/sbin/lvmchange
lvm2 /usr/sbin/lvmconf
lvm2 /usr/sbin/lvmdiskscan
lvm2 /usr/sbin/lvmdump
lvm2 /usr/sbin/lvmetad
lvm2 /usr/sbin/lvmsadc
lvm2 /usr/sbin/lvmsar
lvm2 /usr/sbin/lvreduce
lvm2 /usr/sbin/lvremove
lvm2 /usr/sbin/lvrename
lvm2 /usr/sbin/lvresize
lvm2 /usr/sbin/lvs
lvm2 /usr/sbin/lvscan
lvm2 /usr/sbin/pvchange
lvm2 /usr/sbin/pvck
lvm2 /usr/sbin/pvcreate
lvm2 /usr/sbin/pvdisplay
lvm2 /usr/sbin/pvmove
lvm2 /usr/sbin/pvremove
lvm2 /usr/sbin/pvresize
lvm2 /usr/sbin/pvs
lvm2 /usr/sbin/pvscan
lvm2 /usr/sbin/vgcfgbackup
lvm2 /usr/sbin/vgcfgrestore
lvm2 /usr/sbin/vgchange
lvm2 /usr/sbin/vgck
lvm2 /usr/sbin/vgconvert
lvm2 /usr/sbin/vgcreate
lvm2 /usr/sbin/vgdisplay
lvm2 /usr/sbin/vgexport
lvm2 /usr/sbin/vgextend
lvm2 /usr/sbin/vgimport
lvm2 /usr/sbin/vgimportclone
lvm2 /usr/sbin/vgmerge
lvm2 /usr/sbin/vgmknodes
lvm2 /usr/sbin/vgreduce
lvm2 /usr/sbin/vgremove
lvm2 /usr/sbin/vgrename
lvm2 /usr/sbin/vgs
lvm2 /usr/sbin/vgscan
lvm2 /usr/sbin/vgsplit
man-db /usr/sbin/
man-db /usr/sbin/accessdb
mdadm /sbin/
mdadm /sbin/mdadm
mdadm /sbin/mdassemble
mdadm /sbin/mdmon
modemmanager /usr/sbin/
modemmanager /usr/sbin/ModemManager
net-tools /bin/
net-tools /bin/netstat
net-tools /sbin/
net-tools /sbin/arp
net-tools /sbin/ifconfig
net-tools /sbin/ipmaddr
net-tools /sbin/iptunnel
net-tools /sbin/mii-tool
net-tools /sbin/nameif
net-tools /sbin/plipconfig
net-tools /sbin/rarp
net-tools /sbin/route
net-tools /sbin/slattach
networkmanager /usr/sbin/
networkmanager /usr/sbin/NetworkManager
openssh /usr/sbin/
openssh /usr/sbin/sshd
pam /sbin/
pam /sbin/mkhomedir_helper
pam /sbin/pam_tally
pam /sbin/pam_tally2
pam /sbin/pam_timestamp_check
pam /sbin/unix_chkpwd
pam /sbin/unix_update
parted /usr/sbin/
parted /usr/sbin/parted
parted /usr/sbin/partprobe
pciutils /usr/sbin/
pciutils /usr/sbin/lspci
pciutils /usr/sbin/setpci
pm-utils /usr/sbin/
pm-utils /usr/sbin/pm-hibernate
pm-utils /usr/sbin/pm-powersave
pm-utils /usr/sbin/pm-suspend
pm-utils /usr/sbin/pm-suspend-hybrid
ppp /usr/sbin/
ppp /usr/sbin/chat
ppp /usr/sbin/plog
ppp /usr/sbin/pppd
ppp /usr/sbin/pppdump
ppp /usr/sbin/pppoe-discovery
ppp /usr/sbin/pppstats
procps-ng /bin/
procps-ng /bin/ps
procps-ng /sbin/
procps-ng /sbin/sysctl
reiserfsprogs /sbin/
reiserfsprogs /sbin/debugreiserfs
reiserfsprogs /sbin/fsck.reiserfs
reiserfsprogs /sbin/mkfs.reiserfs
reiserfsprogs /sbin/mkreiserfs
reiserfsprogs /sbin/reiserfsck
reiserfsprogs /sbin/reiserfstune
reiserfsprogs /sbin/resize_reiserfs
rtmpdump /usr/sbin/
rtmpdump /usr/sbin/rtmpgw
rtmpdump /usr/sbin/rtmpsrv
rtmpdump /usr/sbin/rtmpsuck
sed /bin/
sed /bin/sed
shadow /bin/
shadow /bin/groups
shadow /sbin/
shadow /sbin/nologin
shadow /usr/sbin/
shadow /usr/sbin/chgpasswd
shadow /usr/sbin/chpasswd
shadow /usr/sbin/groupadd
shadow /usr/sbin/groupdel
shadow /usr/sbin/groupmems
shadow /usr/sbin/groupmod
shadow /usr/sbin/grpck
shadow /usr/sbin/grpconv
shadow /usr/sbin/grpunconv
shadow /usr/sbin/newusers
shadow /usr/sbin/pwck
shadow /usr/sbin/pwconv
shadow /usr/sbin/pwunconv
shadow /usr/sbin/useradd
shadow /usr/sbin/userdel
shadow /usr/sbin/usermod
systemd /sbin/
systemd /sbin/udevadm
systemd-sysvcompat /sbin/
systemd-sysvcompat /sbin/halt
systemd-sysvcompat /sbin/init
systemd-sysvcompat /sbin/poweroff
systemd-sysvcompat /sbin/reboot
systemd-sysvcompat /sbin/runlevel
systemd-sysvcompat /sbin/shutdown
systemd-sysvcompat /sbin/telinit
sysvinit-tools /bin/
sysvinit-tools /bin/pidof
sysvinit-tools /sbin/
sysvinit-tools /sbin/bootlogd
sysvinit-tools /sbin/fstab-decode
sysvinit-tools /sbin/killall5
tar /bin/
tar /bin/tar
tcpdump /usr/sbin/
tcpdump /usr/sbin/tcpdump
udisks2 /usr/sbin/
udisks2 /usr/sbin/umount.udisks2
usbmuxd /usr/sbin/
usbmuxd /usr/sbin/usbmuxd
util-linux /bin/
util-linux /bin/dmesg
util-linux /bin/findmnt
util-linux /bin/kill
util-linux /bin/login
util-linux /bin/lsblk
util-linux /bin/more
util-linux /bin/mount
util-linux /bin/mountpoint
util-linux /bin/su
util-linux /bin/umount
util-linux /bin/wdctl
util-linux /sbin/
util-linux /sbin/agetty
util-linux /sbin/blkdiscard
util-linux /sbin/blkid
util-linux /sbin/blockdev
util-linux /sbin/cfdisk
util-linux /sbin/chcpu
util-linux /sbin/ctrlaltdel
util-linux /sbin/fdisk
util-linux /sbin/findfs
util-linux /sbin/fsck
util-linux /sbin/fsck.cramfs
util-linux /sbin/fsck.minix
util-linux /sbin/fsfreeze
util-linux /sbin/fstrim
util-linux /sbin/hwclock
util-linux /sbin/losetup
util-linux /sbin/mkfs
util-linux /sbin/mkfs.bfs
util-linux /sbin/mkfs.cramfs
util-linux /sbin/mkfs.minix
util-linux /sbin/mkswap
util-linux /sbin/pivot_root
util-linux /sbin/raw
util-linux /sbin/runuser
util-linux /sbin/sfdisk
util-linux /sbin/sulogin
util-linux /sbin/swaplabel
util-linux /sbin/swapoff
util-linux /sbin/swapon
util-linux /sbin/switch_root
util-linux /sbin/wipefs
util-linux /usr/sbin/
util-linux /usr/sbin/addpart
util-linux /usr/sbin/delpart
util-linux /usr/sbin/fdformat
util-linux /usr/sbin/ldattach
util-linux /usr/sbin/partx
util-linux /usr/sbin/readprofile
util-linux /usr/sbin/resizepart
util-linux /usr/sbin/rtcwake
util-linux /usr/sbin/uuidd
util-linux /usr/sbin/vigr
util-linux /usr/sbin/vipw
v4l-utils /usr/sbin/
v4l-utils /usr/sbin/v4l2-dbg
wireless_tools /usr/sbin/
wireless_tools /usr/sbin/ifrename
wireless_tools /usr/sbin/iwconfig
wireless_tools /usr/sbin/iwevent
wireless_tools /usr/sbin/iwgetid
wireless_tools /usr/sbin/iwlist
wireless_tools /usr/sbin/iwpriv
wireless_tools /usr/sbin/iwspy
wpa_supplicant /usr/sbin/
wpa_supplicant /usr/sbin/wpa_cli
wpa_supplicant /usr/sbin/wpa_passphrase
wpa_supplicant /usr/sbin/wpa_supplicant
xfsprogs /sbin/
xfsprogs /sbin/fsck.xfs
xfsprogs /sbin/mkfs.xfs
xfsprogs /sbin/xfs_repair
xfsprogs /usr/sbin/
xfsprogs /usr/sbin/xfs_admin
xfsprogs /usr/sbin/xfs_bmap
xfsprogs /usr/sbin/xfs_check
xfsprogs /usr/sbin/xfs_copy
xfsprogs /usr/sbin/xfs_db
xfsprogs /usr/sbin/xfs_estimate
xfsprogs /usr/sbin/xfs_freeze
xfsprogs /usr/sbin/xfs_fsr
xfsprogs /usr/sbin/xfs_growfs
xfsprogs /usr/sbin/xfs_info
xfsprogs /usr/sbin/xfs_io
xfsprogs /usr/sbin/xfs_logprint
xfsprogs /usr/sbin/xfs_mdrestore
xfsprogs /usr/sbin/xfs_metadump
xfsprogs /usr/sbin/xfs_mkfile
xfsprogs /usr/sbin/xfs_ncheck
xfsprogs /usr/sbin/xfs_quota
xfsprogs /usr/sbin/xfs_rtcp
xinetd /usr/sbin/
xinetd /usr/sbin/itox
xinetd /usr/sbin/xconv.pl
xinetd /usr/sbin/xinetd
zvbi /usr/sbin/
zvbi /usr/sbin/zvbid

With that output, I'm guessing you don't have anything from that repo actually installed? If that's the case, skip it.

Last edited by Scimmia (2013-07-04 04:04:24)

Offline

#764 2013-07-04 04:05:24

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

Sorry about that.  I'm just a bit confused about what I'm supposed to be doing here.  When the front page instructs me to "fix" the packages, this means to update the packages individually before updating the system?  I tried this:

$ sudo pacman -S grub-common
resolving dependencies...
looking for inter-conflicts...
:: grub and grub-common are in conflict. Remove grub-common? [y/N]

That to me is not indicative of a fix.  Am I on the right path here or have I made a mistake?

Offline

#765 2013-07-04 04:14:17

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

Don't do anything with it specifically. That question will be asked in step 5 (pacman -Syu --ignore filesystem,bash), at which time you should answer yes.

To clarify, those instructions were written before the change in Grub. With this change, grub-common is now a false positive, so to speak.

Last edited by Scimmia (2013-07-04 04:15:34)

Offline

#766 2013-07-04 04:39:59

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

Oh ok.  But I will need to update all of the packages from the catalyst repo per this one liner in step 1

paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

In my case catalyst being the <repo> in question.  I'm also using xorg113 but the above line returns nothing when xorg113 is substituted for <repo>.

So just to clarify, as per this:

$ paclist catalyst | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
apache /usr/sbin/
apache /usr/sbin/ab
apache /usr/sbin/apachectl
apache /usr/sbin/apxs
apache /usr/sbin/checkgid
apache /usr/sbin/dbmmanage
apache /usr/sbin/envvars
apache /usr/sbin/envvars-std
apache /usr/sbin/htcacheclean
apache /usr/sbin/htdbm
apache /usr/sbin/htdigest
apache /usr/sbin/htpasswd
apache /usr/sbin/httpd
apache /usr/sbin/httpd.itk
apache /usr/sbin/httpd.worker
apache /usr/sbin/httxt2dbm
apache /usr/sbin/logresolve
apache /usr/sbin/rotatelogs
apache /usr/sbin/suexec
avahi /usr/sbin/
avahi /usr/sbin/avahi-autoipd
avahi /usr/sbin/avahi-daemon
avahi /usr/sbin/avahi-dnsconfd
bash /bin/
bash /bin/bash
bash /bin/sh
bluez /usr/sbin/
bluez /usr/sbin/bccmd
bluez /usr/sbin/bluetoothd
bluez /usr/sbin/hciattach
bluez /usr/sbin/hciconfig
catalyst-utils /usr/sbin/
catalyst-utils /usr/sbin/amdnotifyui
catalyst-utils /usr/sbin/atieventsd
catalyst-utils /usr/sbin/atigetsysteminfo.sh
cdrkit /usr/sbin/
cdrkit /usr/sbin/netscsid
cifs-utils /usr/sbin/
cifs-utils /usr/sbin/cifs.idmap
cifs-utils /usr/sbin/cifs.upcall
coreutils /bin/
coreutils /bin/cat
coreutils /bin/chgrp
coreutils /bin/chmod
coreutils /bin/chown
coreutils /bin/cp
coreutils /bin/date
coreutils /bin/dd
coreutils /bin/df
coreutils /bin/echo
coreutils /bin/false
coreutils /bin/ln
coreutils /bin/ls
coreutils /bin/mkdir
coreutils /bin/mknod
coreutils /bin/mv
coreutils /bin/pwd
coreutils /bin/rm
coreutils /bin/rmdir
coreutils /bin/stty
coreutils /bin/sync
coreutils /bin/true
coreutils /bin/uname
cracklib /usr/sbin/
cracklib /usr/sbin/cracklib-check
cracklib /usr/sbin/cracklib-format
cracklib /usr/sbin/cracklib-packer
cracklib /usr/sbin/cracklib-unpacker
cracklib /usr/sbin/create-cracklib-dict
cronie /usr/sbin/
cronie /usr/sbin/anacron
cronie /usr/sbin/crond
cryptsetup /usr/sbin/
cryptsetup /usr/sbin/cryptsetup
cryptsetup /usr/sbin/cryptsetup-reencrypt
cryptsetup /usr/sbin/veritysetup
device-mapper /usr/sbin/
device-mapper /usr/sbin/dmeventd
device-mapper /usr/sbin/dmsetup
dhclient /sbin/
dhclient /sbin/dhclient-script
dhclient /usr/sbin/
dhclient /usr/sbin/dhclient
dhcpcd /sbin/
dhcpcd /sbin/dhcpcd
dhcpcd /usr/sbin/
dhcpcd /usr/sbin/dhcpcd
e2fsprogs /sbin/
e2fsprogs /sbin/badblocks
e2fsprogs /sbin/debugfs
e2fsprogs /sbin/dumpe2fs
e2fsprogs /sbin/e2fsck
e2fsprogs /sbin/e2image
e2fsprogs /sbin/e2label
e2fsprogs /sbin/e2undo
e2fsprogs /sbin/fsck.ext2
e2fsprogs /sbin/fsck.ext3
e2fsprogs /sbin/fsck.ext4
e2fsprogs /sbin/fsck.ext4dev
e2fsprogs /sbin/logsave
e2fsprogs /sbin/mke2fs
e2fsprogs /sbin/mkfs.ext2
e2fsprogs /sbin/mkfs.ext3
e2fsprogs /sbin/mkfs.ext4
e2fsprogs /sbin/mkfs.ext4dev
e2fsprogs /sbin/resize2fs
e2fsprogs /sbin/tune2fs
e2fsprogs /usr/sbin/
e2fsprogs /usr/sbin/e2freefrag
e2fsprogs /usr/sbin/e4defrag
e2fsprogs /usr/sbin/filefrag
e2fsprogs /usr/sbin/mklost+found
filesystem /usr/sbin/
fuse /bin/
fuse /bin/fusermount
fuse /bin/ulockmgr_server
fuse /sbin/
fuse /sbin/mount.fuse
gawk /bin/
gawk /bin/awk
gawk /bin/gawk
gconf /usr/sbin/
gconf /usr/sbin/gconfpkg
gdm /usr/sbin/
gdm /usr/sbin/gdm
glibc /sbin/
glibc /sbin/ldconfig
glibc /sbin/sln
glibc /usr/sbin/
glibc /usr/sbin/iconvconfig
glibc /usr/sbin/nscd
glibc /usr/sbin/zdump
glibc /usr/sbin/zic
gpm /usr/sbin/
gpm /usr/sbin/gpm
grub-common /usr/sbin/
grub-common /usr/sbin/grub-bios-setup
grub-common /usr/sbin/grub-install
grub-common /usr/sbin/grub-mkconfig
grub-common /usr/sbin/grub-mknetdir
grub-common /usr/sbin/grub-ofpathname
grub-common /usr/sbin/grub-probe
grub-common /usr/sbin/grub-reboot
grub-common /usr/sbin/grub-set-default
grub-common /usr/sbin/grub-sparc64-setup
icu /usr/sbin/
icu /usr/sbin/genccode
icu /usr/sbin/gencmn
icu /usr/sbin/gennorm2
icu /usr/sbin/gensprep
icu /usr/sbin/icupkg
inetutils /bin/
inetutils /bin/dnsdomainname
inetutils /bin/hostname
iproute2 /sbin/
iproute2 /sbin/ip
iproute2 /usr/sbin/
iproute2 /usr/sbin/arpd
iproute2 /usr/sbin/bridge
iproute2 /usr/sbin/ctstat
iproute2 /usr/sbin/genl
iproute2 /usr/sbin/ifcfg
iproute2 /usr/sbin/ifstat
iproute2 /usr/sbin/ip
iproute2 /usr/sbin/lnstat
iproute2 /usr/sbin/nstat
iproute2 /usr/sbin/routef
iproute2 /usr/sbin/routel
iproute2 /usr/sbin/rtacct
iproute2 /usr/sbin/rtmon
iproute2 /usr/sbin/rtpr
iproute2 /usr/sbin/rtstat
iproute2 /usr/sbin/ss
iproute2 /usr/sbin/tc
iptables /usr/sbin/
iptables /usr/sbin/ip6tables
iptables /usr/sbin/ip6tables-restore
iptables /usr/sbin/ip6tables-save
iptables /usr/sbin/iptables
iptables /usr/sbin/iptables-restore
iptables /usr/sbin/iptables-save
iptables /usr/sbin/xtables-multi
jfsutils /sbin/
jfsutils /sbin/fsck.jfs
jfsutils /sbin/jfs_debugfs
jfsutils /sbin/jfs_fsck
jfsutils /sbin/jfs_fscklog
jfsutils /sbin/jfs_logdump
jfsutils /sbin/jfs_mkfs
jfsutils /sbin/jfs_tune
jfsutils /sbin/mkfs.jfs
kmod /sbin/
kmod /sbin/depmod
kmod /sbin/modprobe
libatasmart /usr/sbin/
libatasmart /usr/sbin/skdump
libatasmart /usr/sbin/sktest
libbonobo /usr/sbin/
libbonobo /usr/sbin/bonobo-activation-sysconf
libsasl /usr/sbin/
libsasl /usr/sbin/pluginviewer
libsasl /usr/sbin/sasldblistusers2
libsasl /usr/sbin/saslpasswd2
lirc-utils /usr/sbin/
lirc-utils /usr/sbin/lircd
lirc-utils /usr/sbin/lircmd
lsof /usr/sbin/
lsof /usr/sbin/lsof
lvm2 /usr/sbin/
lvm2 /usr/sbin/blkdeactivate
lvm2 /usr/sbin/fsadm
lvm2 /usr/sbin/lvchange
lvm2 /usr/sbin/lvconvert
lvm2 /usr/sbin/lvcreate
lvm2 /usr/sbin/lvdisplay
lvm2 /usr/sbin/lvextend
lvm2 /usr/sbin/lvm
lvm2 /usr/sbin/lvmchange
lvm2 /usr/sbin/lvmconf
lvm2 /usr/sbin/lvmdiskscan
lvm2 /usr/sbin/lvmdump
lvm2 /usr/sbin/lvmetad
lvm2 /usr/sbin/lvmsadc
lvm2 /usr/sbin/lvmsar
lvm2 /usr/sbin/lvreduce
lvm2 /usr/sbin/lvremove
lvm2 /usr/sbin/lvrename
lvm2 /usr/sbin/lvresize
lvm2 /usr/sbin/lvs
lvm2 /usr/sbin/lvscan
lvm2 /usr/sbin/pvchange
lvm2 /usr/sbin/pvck
lvm2 /usr/sbin/pvcreate
lvm2 /usr/sbin/pvdisplay
lvm2 /usr/sbin/pvmove
lvm2 /usr/sbin/pvremove
lvm2 /usr/sbin/pvresize
lvm2 /usr/sbin/pvs
lvm2 /usr/sbin/pvscan
lvm2 /usr/sbin/vgcfgbackup
lvm2 /usr/sbin/vgcfgrestore
lvm2 /usr/sbin/vgchange
lvm2 /usr/sbin/vgck
lvm2 /usr/sbin/vgconvert
lvm2 /usr/sbin/vgcreate
lvm2 /usr/sbin/vgdisplay
lvm2 /usr/sbin/vgexport
lvm2 /usr/sbin/vgextend
lvm2 /usr/sbin/vgimport
lvm2 /usr/sbin/vgimportclone
lvm2 /usr/sbin/vgmerge
lvm2 /usr/sbin/vgmknodes
lvm2 /usr/sbin/vgreduce
lvm2 /usr/sbin/vgremove
lvm2 /usr/sbin/vgrename
lvm2 /usr/sbin/vgs
lvm2 /usr/sbin/vgscan
lvm2 /usr/sbin/vgsplit
man-db /usr/sbin/
man-db /usr/sbin/accessdb
mdadm /sbin/
mdadm /sbin/mdadm
mdadm /sbin/mdassemble
mdadm /sbin/mdmon
modemmanager /usr/sbin/
modemmanager /usr/sbin/ModemManager
net-tools /bin/
net-tools /bin/netstat
net-tools /sbin/
net-tools /sbin/arp
net-tools /sbin/ifconfig
net-tools /sbin/ipmaddr
net-tools /sbin/iptunnel
net-tools /sbin/mii-tool
net-tools /sbin/nameif
net-tools /sbin/plipconfig
net-tools /sbin/rarp
net-tools /sbin/route
net-tools /sbin/slattach
networkmanager /usr/sbin/
networkmanager /usr/sbin/NetworkManager
openssh /usr/sbin/
openssh /usr/sbin/sshd
pam /sbin/
pam /sbin/mkhomedir_helper
pam /sbin/pam_tally
pam /sbin/pam_tally2
pam /sbin/pam_timestamp_check
pam /sbin/unix_chkpwd
pam /sbin/unix_update
parted /usr/sbin/
parted /usr/sbin/parted
parted /usr/sbin/partprobe
pciutils /usr/sbin/
pciutils /usr/sbin/lspci
pciutils /usr/sbin/setpci
pm-utils /usr/sbin/
pm-utils /usr/sbin/pm-hibernate
pm-utils /usr/sbin/pm-powersave
pm-utils /usr/sbin/pm-suspend
pm-utils /usr/sbin/pm-suspend-hybrid
ppp /usr/sbin/
ppp /usr/sbin/chat
ppp /usr/sbin/plog
ppp /usr/sbin/pppd
ppp /usr/sbin/pppdump
ppp /usr/sbin/pppoe-discovery
ppp /usr/sbin/pppstats
procps-ng /bin/
procps-ng /bin/ps
procps-ng /sbin/
procps-ng /sbin/sysctl
reiserfsprogs /sbin/
reiserfsprogs /sbin/debugreiserfs
reiserfsprogs /sbin/fsck.reiserfs
reiserfsprogs /sbin/mkfs.reiserfs
reiserfsprogs /sbin/mkreiserfs
reiserfsprogs /sbin/reiserfsck
reiserfsprogs /sbin/reiserfstune
reiserfsprogs /sbin/resize_reiserfs
rtmpdump /usr/sbin/
rtmpdump /usr/sbin/rtmpgw
rtmpdump /usr/sbin/rtmpsrv
rtmpdump /usr/sbin/rtmpsuck
sed /bin/
sed /bin/sed
shadow /bin/
shadow /bin/groups
shadow /sbin/
shadow /sbin/nologin
shadow /usr/sbin/
shadow /usr/sbin/chgpasswd
shadow /usr/sbin/chpasswd
shadow /usr/sbin/groupadd
shadow /usr/sbin/groupdel
shadow /usr/sbin/groupmems
shadow /usr/sbin/groupmod
shadow /usr/sbin/grpck
shadow /usr/sbin/grpconv
shadow /usr/sbin/grpunconv
shadow /usr/sbin/newusers
shadow /usr/sbin/pwck
shadow /usr/sbin/pwconv
shadow /usr/sbin/pwunconv
shadow /usr/sbin/useradd
shadow /usr/sbin/userdel
shadow /usr/sbin/usermod
systemd /sbin/
systemd /sbin/udevadm
systemd-sysvcompat /sbin/
systemd-sysvcompat /sbin/halt
systemd-sysvcompat /sbin/init
systemd-sysvcompat /sbin/poweroff
systemd-sysvcompat /sbin/reboot
systemd-sysvcompat /sbin/runlevel
systemd-sysvcompat /sbin/shutdown
systemd-sysvcompat /sbin/telinit
sysvinit-tools /bin/
sysvinit-tools /bin/pidof
sysvinit-tools /sbin/
sysvinit-tools /sbin/bootlogd
sysvinit-tools /sbin/fstab-decode
sysvinit-tools /sbin/killall5
tar /bin/
tar /bin/tar
tcpdump /usr/sbin/
tcpdump /usr/sbin/tcpdump
udisks2 /usr/sbin/
udisks2 /usr/sbin/umount.udisks2
usbmuxd /usr/sbin/
usbmuxd /usr/sbin/usbmuxd
util-linux /bin/
util-linux /bin/dmesg
util-linux /bin/findmnt
util-linux /bin/kill
util-linux /bin/login
util-linux /bin/lsblk
util-linux /bin/more
util-linux /bin/mount
util-linux /bin/mountpoint
util-linux /bin/su
util-linux /bin/umount
util-linux /bin/wdctl
util-linux /sbin/
util-linux /sbin/agetty
util-linux /sbin/blkdiscard
util-linux /sbin/blkid
util-linux /sbin/blockdev
util-linux /sbin/cfdisk
util-linux /sbin/chcpu
util-linux /sbin/ctrlaltdel
util-linux /sbin/fdisk
util-linux /sbin/findfs
util-linux /sbin/fsck
util-linux /sbin/fsck.cramfs
util-linux /sbin/fsck.minix
util-linux /sbin/fsfreeze
util-linux /sbin/fstrim
util-linux /sbin/hwclock
util-linux /sbin/losetup
util-linux /sbin/mkfs
util-linux /sbin/mkfs.bfs
util-linux /sbin/mkfs.cramfs
util-linux /sbin/mkfs.minix
util-linux /sbin/mkswap
util-linux /sbin/pivot_root
util-linux /sbin/raw
util-linux /sbin/runuser
util-linux /sbin/sfdisk
util-linux /sbin/sulogin
util-linux /sbin/swaplabel
util-linux /sbin/swapoff
util-linux /sbin/swapon
util-linux /sbin/switch_root
util-linux /sbin/wipefs
util-linux /usr/sbin/
util-linux /usr/sbin/addpart
util-linux /usr/sbin/delpart
util-linux /usr/sbin/fdformat
util-linux /usr/sbin/ldattach
util-linux /usr/sbin/partx
util-linux /usr/sbin/readprofile
util-linux /usr/sbin/resizepart
util-linux /usr/sbin/rtcwake
util-linux /usr/sbin/uuidd
util-linux /usr/sbin/vigr
util-linux /usr/sbin/vipw
v4l-utils /usr/sbin/
v4l-utils /usr/sbin/v4l2-dbg
wireless_tools /usr/sbin/
wireless_tools /usr/sbin/ifrename
wireless_tools /usr/sbin/iwconfig
wireless_tools /usr/sbin/iwevent
wireless_tools /usr/sbin/iwgetid
wireless_tools /usr/sbin/iwlist
wireless_tools /usr/sbin/iwpriv
wireless_tools /usr/sbin/iwspy
wpa_supplicant /usr/sbin/
wpa_supplicant /usr/sbin/wpa_cli
wpa_supplicant /usr/sbin/wpa_passphrase
wpa_supplicant /usr/sbin/wpa_supplicant
xfsprogs /sbin/
xfsprogs /sbin/fsck.xfs
xfsprogs /sbin/mkfs.xfs
xfsprogs /sbin/xfs_repair
xfsprogs /usr/sbin/
xfsprogs /usr/sbin/xfs_admin
xfsprogs /usr/sbin/xfs_bmap
xfsprogs /usr/sbin/xfs_check
xfsprogs /usr/sbin/xfs_copy
xfsprogs /usr/sbin/xfs_db
xfsprogs /usr/sbin/xfs_estimate
xfsprogs /usr/sbin/xfs_freeze
xfsprogs /usr/sbin/xfs_fsr
xfsprogs /usr/sbin/xfs_growfs
xfsprogs /usr/sbin/xfs_info
xfsprogs /usr/sbin/xfs_io
xfsprogs /usr/sbin/xfs_logprint
xfsprogs /usr/sbin/xfs_mdrestore
xfsprogs /usr/sbin/xfs_metadump
xfsprogs /usr/sbin/xfs_mkfile
xfsprogs /usr/sbin/xfs_ncheck
xfsprogs /usr/sbin/xfs_quota
xfsprogs /usr/sbin/xfs_rtcp
xinetd /usr/sbin/
xinetd /usr/sbin/itox
xinetd /usr/sbin/xconv.pl
xinetd /usr/sbin/xinetd
zvbi /usr/sbin/
zvbi /usr/sbin/zvbid

I need to update the following (or "fix" according to the news) before moving on to step 5:

$ paclist catalyst | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/' | awk '{print $1}' | sort -u
apache
avahi
bash
bluez
catalyst-utils
cdrkit
cifs-utils
coreutils
cracklib
cronie
cryptsetup
device-mapper
dhclient
dhcpcd
e2fsprogs
filesystem
fuse
gawk
gconf
gdm
glibc
gpm
grub-common
icu
inetutils
iproute2
iptables
jfsutils
kmod
libatasmart
libbonobo
libsasl
lirc-utils
lsof
lvm2
man-db
mdadm
modemmanager
net-tools
networkmanager
openssh
pam
parted
pciutils
pm-utils
ppp
procps-ng
reiserfsprogs
rtmpdump
sed
shadow
systemd
systemd-sysvcompat
sysvinit-tools
tar
tcpdump
udisks2
usbmuxd
util-linux
v4l-utils
wireless_tools
wpa_supplicant
xfsprogs
xinetd
zvbi

So running pacman -s on each of these before moving on to step 5 (assuming steps 2, 3, and 4 require no intervention) should theoretically put me in a safe position to proceed to step 5 and not have to spend the 4th of july chrooting into a broken install and googling on my smartphone?

Offline

#767 2013-07-04 04:52:26

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

No, that's invalid output unless each of those package on your system came from the catalyst repo.

Do you actually have anything from that repo installed? If you don't, paclist returns nothing, so nothing is passed to pacman -Ql, so it reverts to it's default behavior of listing every package on the system.

Try just running pacman -Sl catalyst to see all package available in that repo. Those that are installed will say [Installed] after them.

Last edited by Scimmia (2013-07-04 04:57:02)

Offline

#768 2013-07-04 04:57:29

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

I'm using the proprietary catalyst driver for my radeon graphics card.  Here is man 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/
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   =
#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

[xorg113]
Server = http://catalyst.wirephire.com/repo/xorg113/$arch

[catalyst]
Server = http://catalyst.wirephire.com/repo/catalyst/$arch

[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

# 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

Offline

#769 2013-07-04 05:05:42

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

Sorry, I edited my last post while you were posting.

Try just running pacman -Sl catalyst to see all package available in that repo. Those that are installed will say [Installed] after them.

Also try breaking down that command into parts. Start with just "paclist catalyst", which should return a list of the packages installed from the catalyst repo.

Offline

#770 2013-07-04 05:15:31

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

Hmmm... interesting

$ pacman -Sl catalyst | grep installed
catalyst catalyst 13.6-2 [installed: 13.4-2]
catalyst catalyst-utils 13.6-3 [installed: 13.4-1]

vs

$ paclist catalyst
$ 

Offline

#771 2013-07-04 05:19:31

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

well isn't that fun. How about this replace "paclist catalyst | awk ' { print $1 } '" with "pacman -Sl catalyst | grep installed | awk ' { print $2 }'" in that command. Just another way of getting the same output.

Offline

#772 2013-07-04 05:23:31

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

So should I assume from this

$ pacman -Sl catalyst | grep installed | awk ' { print $2 }'
catalyst
catalyst-utils

That updating these two packages will have me good to go to move on to the last step?  (the other steps needed no intervention)

Offline

#773 2013-07-04 05:25:50

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

sorry, I meant to put that into the command, ie to pipe that to pacman -Qm and grep. This will tell you if either of those packages have files in the dirs in question.

Offline

#774 2013-07-04 05:38:34

instantaphex
Member
Registered: 2012-07-07
Posts: 67

Re: filesystem Update Error /bin exists in filesystem

like this?

$ pacman -Sl catalyst | grep installed | awk '{print $2}' | pacman -Qm -

if so, that returns nothing.  Without the hyphen at the end I get a bunch of stuff.  Including things like mysql, compiz, gnome-games, etc... I definitely didn't get those from the catalyst repos...

Offline

#775 2013-07-04 05:43:04

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,712

Re: filesystem Update Error /bin exists in filesystem

sorry, typo, I meant -Ql, not -Qm

What I'm saying is that "pacman -Sl catalyst | grep installed | awk ' { print $2 }'" will have the same output as "paclist catalyst | awk ' { print $1 } '". Since paclist isn't working on your system for some reason, run the second command from step 1, but substitute in the working command for the not-working part

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