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#1 2013-07-05 15:10:49

gokussjx
Member
Registered: 2013-07-05
Posts: 9

[SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

Hey,

It's been over a week, & I still haven't found a solution to this strange issue. hmm
Whenever I use:

$ sudo pacman -Syu

I'm stuck at the point when all packages are ready to install, and Pacman's checking for file conflicts.

:: Proceed with installation? [Y/n] Y
:: Retrieving packages ...
 libwbclient-4.0.7-3-x86_64                                                                                            28.8 KiB  28.2K/s 00:01 [#######################################################################################] 100%
 smbclient-4.0.7-3-x86_64                                                                                               5.1 MiB  18.4K/s 04:43 [#######################################################################################] 100%
(301/301) checking keys in keyring                                                                                                             [#######################################################################################] 100%
(301/301) checking package integrity                                                                                                           [#######################################################################################] 100%
(301/301) loading package files                                                                                                                [#######################################################################################] 100%
(301/301) checking for file conflicts                                                                                                          [#######################################################################################] 100%

I tried using the --debug parameter to dig some more info, & here's the  latter part of the output:

debug: searching for file conflicts: vim-runtime
debug: searching for filesystem conflicts: vim-runtime
debug: searching for file conflicts: vim
debug: searching for filesystem conflicts: vim
debug: searching for file conflicts: virtualbox-host-dkms
debug: searching for filesystem conflicts: virtualbox-host-dkms
debug: searching for file conflicts: virtualbox-host-modules
debug: searching for filesystem conflicts: virtualbox-host-modules
debug: searching for file conflicts: virtualbox
debug: searching for filesystem conflicts: virtualbox
debug: searching for file conflicts: wine
debug: searching for filesystem conflicts: wine
debug: searching for file conflicts: winetricks
debug: searching for filesystem conflicts: winetricks
debug: searching for file conflicts: wireshark-cli
debug: searching for filesystem conflicts: wireshark-cli
debug: searching for file conflicts: wireshark-gtk
debug: searching for filesystem conflicts: wireshark-gtk
debug: searching for file conflicts: xorg-server-common
debug: searching for filesystem conflicts: xorg-server-common
debug: searching for file conflicts: xorg-server
debug: searching for filesystem conflicts: xorg-server
debug: searching for file conflicts: youtube-dl
debug: searching for filesystem conflicts: youtube-dl
debug: removing conflicting and to-be-replaced packages
removing grub-common...
debug: removing package grub-common-2.00-5
debug: executing ". /tmp/alpm_qmAf2H/.INSTALL; pre_remove 2.00-5"
debug: executing "/usr/bin/bash" under chroot "/"

It hangs at this point permanently, & never budges.

I'm running Arch Linux, KDE 4.10.80, Kernel linux-ck (3.9.9-1-ck) (BFS enabled)

I've tried searching the web (including this forum) for some hints or help, but there's been no direct discussion on this so far.
Please let me know what I can do to fix this. (Or if any additional info required)
Help's really appreciated neutral

Cheers

Last edited by gokussjx (2013-07-06 19:43:32)

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#2 2013-07-06 02:42:29

cfr
Member
From: Cymru
Registered: 2011-11-27
Posts: 7,173

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

Welcome to the forums.

Are you using testing? Your KDE seems to be newer than the version I have installed from stable. What version of bash do you have installed? Is the system entirely up to date (with testing if that's what you're using)?


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#3 2013-07-06 03:41:11

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

cfr wrote:

Welcome to the forums.

Are you using testing? Your KDE seems to be newer than the version I have installed from stable. What version of bash do you have installed? Is the system entirely up to date (with testing if that's what you're using)?

Thank You smile

Yes, I use Testing.
But KDE is Development Version (from KDE-unstable).

My Bash is: GNU bash, version 4.2.45(2)-release

As for the system, the kernel's up-to-date, along with my nvidia drivers. (Manually updated)
But apart from that, the system needs upgrade.
That's exactly why I need help. I've over 2GB worth of updates pending (both KDE updates, & system/user app updates), and pacman hangs at the above stated point.

Any suggestions?

Thanks

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#4 2013-07-06 03:49:37

jasonwryan
Anarchist
From: .nz
Registered: 2009-05-09
Posts: 30,426
Website

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

So you have been doing partial updates?


Arch + dwm   •   Mercurial repos  •   Surfraw

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#5 2013-07-06 03:55:41

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

jasonwryan wrote:

So you have been doing partial updates?

Hey jasonwryan,

I'm guessing not.
I use the following command:

$ sudo pacman -Syy && sudo pacman -Sy && sudo abs && sudo pacman -Syu

(Well, using alias, ofc. pacmir, pacupd & pacupg)

It initializes full system upgrade, gives me update-pending package list, size details, then moves on to checking key, space, conflicts etc.
And hangs at conflict.

This has never been the usual case. I've never faced this issue before.

I've tried re-installing the kernel, rebooting, clearing pacman cache using

$ sudo pacman -Sc

, reinstalling bash & pacman as of now.
Also, commented back the "CheckSpace" in my /etc/pacman.conf file. (It had started to hang at checking available space)

Last edited by gokussjx (2013-07-06 04:01:17)

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#6 2013-07-06 04:32:15

jasonwryan
Anarchist
From: .nz
Registered: 2009-05-09
Posts: 30,426
Website

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

gokussjx wrote:

As for the system, the kernel's up-to-date, along with my nvidia drivers. (Manually updated)
But apart from that, the system needs upgrade.

That looks to me like a partial upgrade.


Have you completed the move of binaries to /usr/bin?


Arch + dwm   •   Mercurial repos  •   Surfraw

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#7 2013-07-06 04:36:13

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

jasonwryan wrote:
gokussjx wrote:

As for the system, the kernel's up-to-date, along with my nvidia drivers. (Manually updated)
But apart from that, the system needs upgrade.

That looks to me like a partial upgrade.


Have you completed the move of binaries to /usr/bin?

You mean the recent big symlink changes?
Yes, my system's updated with those changes.

I'd updated/upgraded as well, & it had worked.

Speaking of Partial Upgrades, will it called a Full Upgrade if I simply use pacman -Syu only?
I've tried using that as well, & the result is same.

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#8 2013-07-06 04:39:38

jasonwryan
Anarchist
From: .nz
Registered: 2009-05-09
Posts: 30,426
Website

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

Your bash is not up-to-date. It would be helpful to see the list of other packages pacman is trying to update.


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#9 2013-07-06 04:41:18

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

jasonwryan wrote:

Your bash is not up-to-date. It would be helpful to see the list iof other packages pacman is trying to update.

Sure:

:: Synchronizing package databases...
 kde-unstable                                                                                                         141.9 KiB  30.5K/s 00:05 [#######################################################################################] 100%
 testing                                                                                                               41.1 KiB  16.4K/s 00:03 [#######################################################################################] 100%
 core                                                                                                                 102.8 KiB  34.9K/s 00:03 [#######################################################################################] 100%
 extra                                                                                                               1436.7 KiB  35.0K/s 00:41 [#######################################################################################] 100%
 community-testing                                                                                                   1213.0   B  0.00B/s 00:00 [#######################################################################################] 100%
 community                                                                                                           1975.7 KiB  17.5K/s 01:53 [#######################################################################################] 100%
 multilib                                                                                                             106.1 KiB  23.8K/s 00:04 [#######################################################################################] 100%
 xyne-any                                                                                                              24.8 KiB  35.2K/s 00:01 [#######################################################################################] 100%
 xyne-any.sig                                                                                                         287.0   B  0.00B/s 00:00 [#######################################################################################] 100%
 xyne-x86_64                                                                                                           28.3 KiB  20.5K/s 00:01 [#######################################################################################] 100%
 xyne-x86_64.sig                                                                                                      287.0   B  0.00B/s 00:00 [#######################################################################################] 100%
 archlinuxfr                                                                                                           14.8 KiB  14.4K/s 00:01 [#######################################################################################] 100%
:: Synchronizing package databases...
 kde-unstable is up to date
 testing is up to date
 core is up to date
 extra is up to date
 community-testing is up to date
 community is up to date
 multilib is up to date
 xyne-any is up to date
 xyne-x86_64 is up to date
 archlinuxfr is up to date
==> Starting ABS sync...
receiving file list ... done

sent 178 bytes  received 347478 bytes  11398.56 bytes/sec
total size is 15862236  speedup is 45.63
:: Synchronizing package databases...
 kde-unstable is up to date
 testing is up to date
 core is up to date
 extra is up to date
 community-testing is up to date
 community is up to date
 multilib is up to date
 xyne-any is up to date
 xyne-x86_64 is up to date
 archlinuxfr is up to date
:: Starting full system upgrade...
:: Replace grub-common with core/grub? [Y/n] Y
resolving dependencies...
looking for inter-conflicts...

Packages (302): automake-1.14-1  cifs-utils-6.1-1  cmake-2.8.11.2-1  colord-1.0.1-1  cronie-1.4.9-5  cups-filters-1.0.35-1  curl-7.31.0-1  dhcpcd-6.0.2-1  e2fsprogs-1.42.8-1  eclipse-cdt-8.2.0-1  ed-1.9-1  filezilla-3.7.1.1-1
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Total Download Size:    5.10 MiB
Total Installed Size:   2364.94 MiB
Net Upgrade Size:       32.96 MiB

:: Proceed with installation? [Y/n] Y
:: Retrieving packages ...
 libwbclient-4.0.7-3-x86_64                                                                                            28.8 KiB  28.2K/s 00:01 [#######################################################################################] 100%
 smbclient-4.0.7-3-x86_64                                                                                               5.1 MiB  18.4K/s 04:43 [#######################################################################################] 100%
(301/301) checking keys in keyring                                                                                                             [#######################################################################################] 100%
(301/301) checking package integrity                                                                                                           [#######################################################################################] 100%
(301/301) loading package files                                                                                                                [#######################################################################################] 100%
(301/301) checking for file conflicts

Strange though... I don't see any bash update yikes

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#10 2013-07-06 05:45:35

apg
Developer
Registered: 2012-11-10
Posts: 211

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

gokussjx wrote:

I use the following command:

$ sudo pacman -Syy && sudo pacman -Sy && sudo abs && sudo pacman -Syu

There's no reason to call pacman three times there, all you're doing is generating a lot of unnecessary output.  Instead, just use a single:

pacman -Syyu
gokussix wrote:
debug: removing package grub-common-2.00-5
debug: executing ". /tmp/alpm_qmAf2H/.INSTALL; pre_remove 2.00-5"
debug: executing "/usr/bin/bash" under chroot "/"

Your upgrade is failing in the grub-common install script, the relevant part of which is:

infodir="usr/share/info"
filelist=('grub.info' 'grub-dev.info')

pre_remove() {
  for file in ${filelist[@]}; do
    install-info --delete ${infodir}/${file} ${infodir}/dir 2> /dev/null
  done
}

Just to make sure the relevant programs are properly installed, can you give the output of

pacman -Q bash texinfo

and

which bash install-info

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#11 2013-07-06 08:43:13

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

apg wrote:

Your upgrade is failing in the grub-common install script, the relevant part of which is:

infodir="usr/share/info"
filelist=('grub.info' 'grub-dev.info')

pre_remove() {
  for file in ${filelist[@]}; do
    install-info --delete ${infodir}/${file} ${infodir}/dir 2> /dev/null
  done
}

Just to make sure the relevant programs are properly installed, can you give the output of

pacman -Q bash texinfo

and

which bash install-info

Hey apg,

Here're the outputs:

bash 4.2.045-4                                                                                                                                               
texinfo 5.1-1

&

/usr/bin/bash                                                                                                                                                
/usr/bin/install-info

Thanks for the info.
Will it work if I manually purge grub & re-install the new grub package?
Or is there something else to be done?


PS:
I tried upgrading without the grub package:

sudo pacman -Syyu --ignore grub grub-common

Superficially, the installation started (FIrst package, automake, was installed), then it hung again.
The error seems to be global.

Here's the last of debug report:

debug: updating database
debug: adding database entry 'e2fsprogs'
debug: writing e2fsprogs-1.42.8-1 DESC information back to db
debug: writing e2fsprogs-1.42.8-1 FILES information back to db
debug: adding entry 'e2fsprogs' in 'local' cache
debug: executing ". /tmp/alpm_4XR11b/.INSTALL; post_upgrade 1.42.8-1 1.42.7-2"
debug: executing "/usr/bin/bash" under chroot "/"

Last edited by gokussjx (2013-07-06 09:24:35)

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#12 2013-07-06 16:25:28

apg
Developer
Registered: 2012-11-10
Posts: 211

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

gokussjx wrote:
bash 4.2.045-4                                                                                                                                               
texinfo 5.1-1

&

/usr/bin/bash                                                                                                                                                
/usr/bin/install-info

Okay, bash and texinfo are up-to-date and in the correct location.

gokussjx wrote:
debug: updating database
debug: adding database entry 'e2fsprogs'
debug: writing e2fsprogs-1.42.8-1 DESC information back to db
debug: writing e2fsprogs-1.42.8-1 FILES information back to db
debug: adding entry 'e2fsprogs' in 'local' cache
debug: executing ". /tmp/alpm_4XR11b/.INSTALL; post_upgrade 1.42.8-1 1.42.7-2"
debug: executing "/usr/bin/bash" under chroot "/"

Unfortunately, that doesn't narrow things down for us much because the e2fsprogs install script is also calling install-info.  Double check that your installed script matches the official package (https://projects.archlinux.org/svntogit … /e2fsprogs) and try running it manually to see if it hangs:

$ cd /
# /usr/bin/bash -c '. /var/lib/pacman/local/e2fsprogs-1.42.8-1/install; post_upgrade 1.42.8-1 1.42.7-2'

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#13 2013-07-06 17:53:23

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

apg wrote:

Unfortunately, that doesn't narrow things down for us much because the e2fsprogs install script is also calling install-info.  Double check that your installed script matches the official package (https://projects.archlinux.org/svntogit … /e2fsprogs) and try running it manually to see if it hangs:

$ cd /
# /usr/bin/bash -c '. /var/lib/pacman/local/e2fsprogs-1.42.8-1/install; post_upgrade 1.42.8-1 1.42.7-2'

I cross-checked the temporary .INSTALL file, for grub, e2fsprogs, ed etc with the project upstream file.
They are perfect match.

Then tried executing the command you listed... Yes, it hangs hmm

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#14 2013-07-06 19:01:26

apg
Developer
Registered: 2012-11-10
Posts: 211

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

Does calling install-info directly hang?

# install-info /usr/share/info/libext2fs.info.gz /usr/share/info/dir

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#15 2013-07-06 19:03:39

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

apg wrote:

Does calling install-info directly hang?

# install-info /usr/share/info/libext2fs.info.gz /usr/share/info/dir

Yes, hangs at that too neutral

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#16 2013-07-06 19:26:57

apg
Developer
Registered: 2012-11-10
Posts: 211

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

gokussjx wrote:
apg wrote:

Does calling install-info directly hang?

# install-info /usr/share/info/libext2fs.info.gz /usr/share/info/dir

Yes, hangs at that too neutral

I'm guessing that something is wrong with either /usr/share/info/dir or install-info.  You can try restoring both by moving dir out of /usr/share/info and reinstalling texinfo:

# mv /usr/share/info/dir <some other directory>
# pacman -S --noscriptlet texinfo
# pacman -S texinfo

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#17 2013-07-06 19:38:59

gokussjx
Member
Registered: 2013-07-05
Posts: 9

Re: [SOLVED]Pacman: Stuck at upgrade "checking for filesystem conflicts"

apg wrote:

I'm guessing that something is wrong with either /usr/share/info/dir or install-info.  You can try restoring both by moving dir out of /usr/share/info and reinstalling texinfo:

# mv /usr/share/info/dir <some other directory>
# pacman -S --noscriptlet texinfo
# pacman -S texinfo

Spot on!
It worked! Installing as usual now. big_smile

Can't thank you enough... Thanks a lot mate!

I'll mark the topic solved.

Cheers!

Last edited by gokussjx (2013-07-06 19:41:03)

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