Pacman error

stev456i · 2009-01-04 19:13:20

I am a noob to Arch. I just installed it via the Chakra Project Live cd. However, when I run this command:

pacman -Syu

I get the following:

pacman -Syu
:: Synchronizing package databases...
kdemod-core is up to date
kdemod-extragear is up to date
kdemod-playground is up to date
core is up to date
extra 386.4K 55.2K/s 00:00:07 [#####################] 100%
community is up to date
:: Starting full system upgrade...
resolving dependencies...
warning: dependency cycle detected:
warning: bash will be installed before its glibc dependency
looking for inter-conflicts...

Targets (76): bash-3.2.048-1 kernel-headers-2.6.27.6-2 glibc-2.9-2
gcc-libs-4.3.2-2 libtasn1-1.7-1 zlib-1.2.3.3-3 gnutls-2.6.3-1
openssl-0.9.8i-3 heimdal-1.2.1-2 libpng-1.2.34-1
libcups-1.3.9-2 xcb-util-0.3.2-1 cairo-1.8.6-1 pango-1.22.4-1
gtk2-2.14.6-1 at-spi-1.24.1-1 avahi-0.6.24-1 binutils-2.19-1
bison-2.4.1-1 ca-certificates-20080809-5 dbus-glib-0.78-1
dhcpcd-4.0.7-1 diffutils-2.8.1-6 sqlite3-3.6.7-2 nss-3.12.2-1
xulrunner-1.9.0.5-2 epiphany-2.24.2.1-2
evolution-data-server-2.24.2-2 fakeroot-1.11.4-1 gcc-4.3.2-2
libxml2-2.7.2-1 gconf-2.24.0-2 gnome-panel-2.24.2-2
gnome-control-center-2.24.0.1-4 gnome-doc-utils-0.14.1-1
gnome-session-2.24.2-2 tdb-3.2.6-2 smbclient-3.2.6-2
gnome-vfs-2.24.0-2 grub-0.97-15 gvfs-1.0.3-2
hal-info-0.20081219-1 hdparm-9.3-1 hwd-5.4.2-1
hwdetect-2008.12-4 intel-dri-7.2-2 kdemod-kdelibs-4.1.3-4
kdemod-kdebase-workspace-4.1.3-5 kernel26-2.6.27.10-1
klibc-udev-135-1 libdmx-1.0.2-2 libexif-0.6.17-1
libgsf-1.14.10-1 libpcap-1.0.0-1 libx86-1.1-2
libxfont-1.3.4-1 loudmouth-1.4.3-1 man-pages-3.15-1
mcpp-2.7.2-1 poppler-0.10.2-1 poppler-qt-0.10.2-1 ppp-2.4.4-7
pycairo-1.8.0-1 qscintilla-2.3.2-2 rsync-3.0.5-1
subversion-1.5.5-1 sudo-1.7.0-1 tar-1.21-1 udev-135-1
vi-7.2.65-1 xextproto-7.0.4-1 xf86-input-evdev-2.1.0-1
xf86-video-vesa-2.1.0-1 xkeyboard-config-1.4-2
xorg-font-utils-7.4-1 xorg-server-1.5.3-4

Total Download Size: 0.00 MB
Total Installed Size: 709.89 MB

Proceed with installation? [Y/n] y
checking package integrity...
(76/76) checking for file conflicts [#####################] 100%
error: could not prepare transaction
error: failed to commit transaction (conflicting files)
bash: /usr/share/info/bash.info exists in filesystem
kernel-headers: /usr/include/..install.cmd exists in filesystem
kernel-headers: /usr/include/.install exists in filesystem
kernel-headers: /usr/include/asm-generic/..install.cmd exists in filesystem
kernel-headers: /usr/include/asm-generic/.install exists in filesystem
kernel-headers: /usr/include/asm/..install.cmd exists in filesystem
kernel-headers: /usr/include/asm/.install exists in filesystem
kernel-headers: /usr/include/linux/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/.install exists in filesystem
kernel-headers: /usr/include/linux/byteorder/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/byteorder/.install exists in filesystem
kernel-headers: /usr/include/linux/can/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/can/.install exists in filesystem
kernel-headers: /usr/include/linux/dvb/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/dvb/.install exists in filesystem
kernel-headers: /usr/include/linux/hdlc/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/hdlc/.install exists in filesystem
kernel-headers: /usr/include/linux/ip_vs.h exists in filesystem
kernel-headers: /usr/include/linux/isdn/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/isdn/.install exists in filesystem
kernel-headers: /usr/include/linux/ivtv.h exists in filesystem
kernel-headers: /usr/include/linux/ivtvfb.h exists in filesystem
kernel-headers: /usr/include/linux/netfilter/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/netfilter/.install exists in filesystem
kernel-headers: /usr/include/linux/netfilter_arp/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/netfilter_arp/.install exists in filesystem
kernel-headers: /usr/include/linux/netfilter_bridge/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/netfilter_bridge/.install exists in filesystem
kernel-headers: /usr/include/linux/netfilter_ipv4/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/netfilter_ipv4/.install exists in filesystem
kernel-headers: /usr/include/linux/netfilter_ipv6/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/netfilter_ipv6/.install exists in filesystem
kernel-headers: /usr/include/linux/nfsd/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/nfsd/.install exists in filesystem
kernel-headers: /usr/include/linux/raid/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/raid/.install exists in filesystem
kernel-headers: /usr/include/linux/spi/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/spi/.install exists in filesystem
kernel-headers: /usr/include/linux/sunrpc/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/sunrpc/.install exists in filesystem
kernel-headers: /usr/include/linux/tc_act/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/tc_act/.install exists in filesystem
kernel-headers: /usr/include/linux/tc_ematch/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/tc_ematch/.install exists in filesystem
kernel-headers: /usr/include/linux/usb/..install.cmd exists in filesystem
kernel-headers: /usr/include/linux/usb/.install exists in filesystem
kernel-headers: /usr/include/linux/virtio_rng.h exists in filesystem
kernel-headers: /usr/include/mtd/..install.cmd exists in filesystem
kernel-headers: /usr/include/mtd/.install exists in filesystem
kernel-headers: /usr/include/rdma/..install.cmd exists in filesystem
kernel-headers: /usr/include/rdma/.install exists in filesystem
kernel-headers: /usr/include/sound/..install.cmd exists in filesystem
kernel-headers: /usr/include/sound/.install exists in filesystem
kernel-headers: /usr/include/video/..install.cmd exists in filesystem
kernel-headers: /usr/include/video/.install exists in filesystem
glibc: /lib/ld-2.9.so exists in filesystem
glibc: /lib/libBrokenLocale-2.9.so exists in filesystem
glibc: /lib/libanl-2.9.so exists in filesystem
glibc: /lib/libc-2.9.so exists in filesystem
glibc: /lib/libcidn-2.9.so exists in filesystem
glibc: /lib/libcrypt-2.9.so exists in filesystem
glibc: /lib/libdl-2.9.so exists in filesystem
glibc: /lib/libm-2.9.so exists in filesystem
glibc: /lib/libnsl-2.9.so exists in filesystem
glibc: /lib/libnss_compat-2.9.so exists in filesystem
glibc: /lib/libnss_dns-2.9.so exists in filesystem
glibc: /lib/libnss_files-2.9.so exists in filesystem
glibc: /lib/libnss_hesiod-2.9.so exists in filesystem
glibc: /lib/libnss_nis-2.9.so exists in filesystem
glibc: /lib/libnss_nisplus-2.9.so exists in filesystem
glibc: /lib/libpthread-2.9.so exists in filesystem
glibc: /lib/libresolv-2.9.so exists in filesystem
glibc: /lib/librt-2.9.so exists in filesystem
glibc: /lib/libutil-2.9.so exists in filesystem
glibc: /usr/share/i18n/locales/en_AG exists in filesystem
glibc: /usr/share/i18n/locales/hne_IN exists in filesystem
glibc: /usr/share/i18n/locales/ht_HT exists in filesystem
glibc: /usr/share/i18n/locales/ks_IN@devanagari exists in filesystem
glibc: /usr/share/i18n/locales/nl_AW exists in filesystem
glibc: /usr/share/i18n/locales/sd_IN exists in filesystem
glibc: /usr/share/i18n/locales/sd_IN@devanagari exists in filesystem
glibc: /usr/share/locale/id/LC_MESSAGES/libc.mo exists in filesystem
glibc: /usr/share/locale/lt/LC_MESSAGES/libc.mo exists in filesystem
heimdal: /usr/lib/libhx509.so.4 exists in filesystem
heimdal: /usr/lib/libhx509.so.4.0.0 exists in filesystem
heimdal: /usr/share/info/heimdal.info.gz exists in filesystem
heimdal: /usr/share/info/hx509.info.gz exists in filesystem
heimdal: /usr/share/man/man5/login.access.5.gz exists in filesystem
binutils: /usr/lib/libbfd-2.19.0.20081119.so exists in filesystem
binutils: /usr/lib/libopcodes-2.19.0.20081119.so exists in filesystem
binutils: /usr/man/man1/addr2line.1.gz exists in filesystem
binutils: /usr/man/man1/ar.1.gz exists in filesystem
binutils: /usr/man/man1/as.1.gz exists in filesystem
binutils: /usr/man/man1/c++filt.1.gz exists in filesystem
binutils: /usr/man/man1/dlltool.1.gz exists in filesystem
binutils: /usr/man/man1/gprof.1.gz exists in filesystem
binutils: /usr/man/man1/ld.1.gz exists in filesystem
binutils: /usr/man/man1/nlmconv.1.gz exists in filesystem
binutils: /usr/man/man1/nm.1.gz exists in filesystem
binutils: /usr/man/man1/objcopy.1.gz exists in filesystem
binutils: /usr/man/man1/objdump.1.gz exists in filesystem
binutils: /usr/man/man1/ranlib.1.gz exists in filesystem
binutils: /usr/man/man1/readelf.1.gz exists in filesystem
binutils: /usr/man/man1/size.1.gz exists in filesystem
binutils: /usr/man/man1/strings.1.gz exists in filesystem
binutils: /usr/man/man1/strip.1.gz exists in filesystem
binutils: /usr/man/man1/windmc.1.gz exists in filesystem
binutils: /usr/man/man1/windres.1.gz exists in filesystem
binutils: /usr/share/locale/fi/LC_MESSAGES/bfd.mo exists in filesystem
binutils: /usr/share/locale/nl/LC_MESSAGES/gprof.mo exists in filesystem
binutils: /usr/share/locale/ro/LC_MESSAGES/gprof.mo exists in filesystem
binutils: /usr/share/locale/sk/LC_MESSAGES/binutils.mo exists in filesystem
dhcpcd: /usr/share/licenses/dhcpcd/LICENSE exists in filesystem
ppp: /usr/share/man/man1/pon.1.gz exists in filesystem
ppp: /usr/share/man/man8/chat.8.gz exists in filesystem
ppp: /usr/share/man/man8/pppd-radattr.8.gz exists in filesystem
ppp: /usr/share/man/man8/pppd-radius.8.gz exists in filesystem
ppp: /usr/share/man/man8/pppd.8.gz exists in filesystem
ppp: /usr/share/man/man8/pppdump.8.gz exists in filesystem
ppp: /usr/share/man/man8/pppstats.8.gz exists in filesystem
vi: /usr/share/vim/indent/cuda.vim exists in filesystem
vi: /usr/share/vim/spell/fixdup.vim exists in filesystem
xf86-input-evdev: /usr/include/xorg/evdev-properties.h exists in filesystem
xf86-input-evdev: /usr/lib/pkgconfig/xorg-evdev.pc exists in filesystem
xf86-input-evdev: /usr/share/licenses/xf86-input-evdev/COPYING exists in filesystem
Errors occurred, no packages were upgraded.

At first I thought it was a Shaman error, but I got it when I tried to upgrade for the command line. Any ideas. I didn't see other threads that I had this same problem, but maybe I missed something.

Thanks.

mcmillan · 2009-01-04 19:29:44

You can figure out if pacman thinks any of those files belongs to something else with pacman -Qo (filename). I suspect it will probably be ok to force the install with pacman -Sf, though if you do this I'd reccommend doing it just for the packages that cause problems and not as pacman -Syuf in case some other problem comes up. I'm not sure what would cause this though, you might want to report it to the chakra people since it popped up after installing with their liveCD.

Xyne · 2009-01-04 19:31:07

Have you tried this: http://www.archlinux.org/news/411/

I would recommend not forcing the install until you've gotten a few replies here.

stev456i · 2009-01-05 01:46:01

Okay, I just tried that:

rm /usr/lib/klibc/include/asm
rm: cannot remove `/usr/lib/klibc/include/asm': Is a directory

so it did not work. I'm still looking and I really don't want to force installs until I am comfortaable about what I am doing.

Thanks so far.

cdwillis · 2009-01-05 02:15:40

Did you run it as root? Try it again and then update.

.:B:. · 2009-01-05 02:21:31

Please gentlemen... One removes directories recursively:

rm -r

Also, one uses the search before posting ones topic, preferably .

Allan · 2009-01-05 03:17:31

Did anyone even read his error message? This has absolutely nothing to do with klibc so I would highly recommend not deleting that folder. That is bad advise. If you have done this already, do a "pacman -S klibc" to get the files back.

The first reply is the way to go. Use "pacman -Sf <pkg>" for each package that is involved. Then do an update of your system.

Edit: I should add that this is very strange. It appears pacman has lost track of many files on your filesystem....

Xyne · 2009-01-05 05:01:38

Sorry, I just saw all the file conflicts and that was the first thing I thought of.

Last edited by Xyne (2009-01-05 05:04:17)

.:B:. · 2009-01-05 16:17:46

Same here

stev456i · 2009-01-05 17:49:52

I dumb and didn't know any better.

Anyways tonight I will try to give it another shot. So I should do the following (as root of course):

pacman -Sf <pkg>

for all of the files/pkgs listed? Or is there a few I should do first?

Thanks for the patience.

ibendiben · 2009-01-05 18:32:52

I think chakra's installer copies those files directly from the life environment to the harddisk, without using pacman. The life filesystem is different form a normal harddisk install, so there are always gaps that need to be covered. Appearantly the installer doesn't cover all the gaps yet, because all those files should be listed in the pacman database. You should report about this to the chakra project.

I think it's ok to pacman -Sf all the packages listed as 'exsisting in filesystem'.

stev456i · 2009-01-08 03:19:03

Okay, I am off and running. I probaly shouldn't have but I ran:

pacman -Sfyu

and everything installed properly.

Thanks again.

funkyou · 2009-01-09 12:06:16

This is weird stuff, you are the first and only one with this problem.

How much ram does your machine have?
Currently the live installer needs at least 384MiB (the more the better) to work correctly. If you have less, the OOM-Killer will most likely appear and kill some random processes

ibendiben wrote:

I think chakra's installer copies those files directly from the life environment to the harddisk, without using pacman. The life filesystem is different form a normal harddisk install, so there are always gaps that need to be covered. Appearantly the installer doesn't cover all the gaps yet, because all those files should be listed in the pacman database. You should report about this to the chakra project.

Yes, it copies the live system directly from the CD. But there are not much gaps, because the live system is split into 3 overlays. Only one of these, the base arch installation without any modifications, will be copied to the target and configured then. Its basically the same as a hdd installation, just totally unconfigured...

Well, lets wait for alpha2, there are many bugs fixed already

edit: typos...

Last edited by funkyou (2009-01-09 13:15:53)

stev456i · 2009-01-10 16:09:57

I have 1gig of ram, so I am good there.

I can only see this project getting better and better.

stev456i · 2009-01-10 21:00:20

Okay here's a new wrinkle. I liked Arch so much, I decided to install in on my main drive. (I did have it on a old hd I use to try different distros). Installed it from the chakra livecd as before, did the upgrade with:

pacman -Syu

and.......everything installed, as it should have! Same machine, except the old drive is a Western digital (about 8-9 years old) and my main one (still old-3-5years) is a Seagate.

So if I'm the only one who experienced this, then so be it. It was just a quirk somehow. I did learn something: that Arch has a great group supporting noobs.
Thanks.

vvlist · 2009-01-11 23:18:54

Arch newbie here, just wanted to say I had the same klibc* update problem, but using

pacman -Sf klibc klibc-extras klibc-kbd klibc-module-init-tools klibc-udev

fixed the issue. I LOVE this distro by the way... Thank you for showing me what a real Linux distro should be. Consider me a convert.

SamC · 2009-01-12 01:06:01

vvlist: That wasn't the right way to go about it, read the news.

cdwillis · 2009-01-12 01:55:17

stev456i, I apologize for my bad advice which could have screwed up your system. I'll be more careful when giving out advice in the future.

Eboogie · 2009-01-13 07:57:56

i had this problem a few mins ago

funkyou · 2009-01-14 17:11:58

Happened for me too after installing alpha1 of chakra on our old Thinkpad and updating afterwards..

Well, now i need some advice, because i cant see a mistake in how we install the system.

Here is what we do during installation:

1 - format and mount all targets
2 - rsync -rlptgo --progress --no-i-r $INSTALL_SOURCE $INSTALL_TARGET
3 - configure the system, e.g. modifying some configs, install grub and running pacman -Sy over it and installing some more packages

$INSTALL_SOURCE is basically a mounted squashfs image containing just an unmodified and clean Arch base install + KDEmod. Everything else, like the modifications for the liveCD are in another overlay...

Maybe someone has an idea why pacman has lost track of these files?

Maybe rsync is the cause here, but i would need some clearance on that. We are planning to replace that by unpacking the squashfs image directly to the target, which should be a lot faster too, but maybe its also a general issue with our approach of installing.

Arch Linux

#1 2009-01-04 19:13:20

Pacman error

#2 2009-01-04 19:29:44

Re: Pacman error

#3 2009-01-04 19:31:07

Re: Pacman error

#4 2009-01-05 01:46:01

Re: Pacman error

#5 2009-01-05 02:15:40

Re: Pacman error

#6 2009-01-05 02:21:31

Re: Pacman error

#7 2009-01-05 03:17:31

Re: Pacman error

#8 2009-01-05 05:01:38

Re: Pacman error

#9 2009-01-05 16:17:46

Re: Pacman error

#10 2009-01-05 17:49:52

Re: Pacman error

#11 2009-01-05 18:32:52

Re: Pacman error

#12 2009-01-08 03:19:03

Re: Pacman error

#13 2009-01-09 12:06:16

Re: Pacman error

#14 2009-01-10 16:09:57

Re: Pacman error

#15 2009-01-10 21:00:20

Re: Pacman error

#16 2009-01-11 23:18:54

Re: Pacman error

#17 2009-01-12 01:06:01

Re: Pacman error

#18 2009-01-12 01:55:17

Re: Pacman error

#19 2009-01-13 07:57:56

Re: Pacman error

#20 2009-01-14 17:11:58

Re: Pacman error

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