Martin Frezman
Posts: 1021
Joined: Mon Oct 31, 2016 10:05 am

Solved: Cannot update system (error about conflicting files)

Wed Jun 14, 2017 8:21 am

Have an Arch system setup with PINN. Haven't booted in a few months. Decided to boot it up today and upgrade system, using command "pacman -Syu". Get error as shown below:

Code: Select all

Script started on Wed Jun 14 04:07:37 2017
[root@alarmpi Progs]# P
[root@alarmpi Progs]# pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 alarm is up to date
 aur is up to date
:: Starting full system upgrade...
:: Replace mesa-libgl with extra/mesa? [Y/n]
resolving dependencies...
looking for conflicting packages...
warning: dependency cycle detected:
warning: libpcap will be installed before its systemd dependency
warning: dependency cycle detected:
warning: harfbuzz will be installed before its freetype2 dependency
warning: dependency cycle detected:
warning: mesa will be installed before its libglvnd dependency

Packages (196) adwaita-icon-theme-3.22.0+1+g58cd459e-1	alsa-lib-1.1.4.1-1  at-spi2-atk-2.24.1-1  at-spi2-core-2.24.1-1	 atk-2.24.0-2  bash-4.4.012-2  binutils-2.28.0-3  busybox-1.26.2-2  bzip2-1.0.6-6
	       ca-certificates-20170307-1  ca-certificates-mozilla-3.31-3  ca-certificates-utils-20170307-1  cifs-utils-6.7-2  coreutils-8.27-1	 cryptsetup-1.7.5-1  curl-7.54.0-3  dbus-1.10.18-1  dconf-0.26.0+1+g701d19d-1
	       device-mapper-2.02.171-1	 dialog-1:1.3_20170509-1  diffutils-3.6-1  dnssec-anchors-20170228-1  e2fsprogs-1.43.4-1  file-5.31-1  filesystem-2017.03-2  fixesproto-5.0+9+g4292ec1-1  fontconfig-2.12.3-1
	       fontsproto-2.1.3-2  freetype2-2.8-2  fuse-common-3.0.2-1	 gcc-7.1.1-2  gcc-libs-7.1.1-2	gdbm-1.13-1  gdk-pixbuf2-2.36.6-2  glib2-2.52.2+9+g3245eba16-1	glibc-2.25-2  gnupg-2.1.21-3  gnutls-3.5.13-1
	       gpgme-1.9.0-3  gpicview-0.2.5-3	graphite-1:1.3.10-1  grep-3.0-1	 gtk-update-icon-cache-3.22.15-1  gtk3-3.22.15-1  gvim-8.0.0628-1  harfbuzz-1.4.6-1  hwids-20170328-1  iana-etc-20170512-1  icu-59.1-1
	       imlib2-1.4.10-1	iproute2-4.11.0-1  iptables-1.6.1-1  iputils-20161105.1f2bb12-2	 jasper-2.0.13-1  json-glib-1.2.8-1  kbd-2.0.4-1  keyutils-1.5.10-1  kmod-24-1	krb5-1.15.1-1  ldns-1.7.0-3  libarchive-3.3.1-5
	       libbsd-0.8.3-2  libcroco-0.6.12+4+g9ad7287-1  libcups-2.2.3-1  libdatrie-0.2.10-2  libdrm-2.4.81-1  libedit-20170329_3.1-1  libelf-0.169-1  libepoxy-1.4.3-1  libevdev-1.5.7-1  libgcrypt-1.7.7-1
	       libglvnd-0.2.999+g4ba53457-2  libgpg-error-1.27-1  libgudev-231+1+g0841288-1  libinput-1.7.3-1  libldap-2.4.44-5	 libnghttp2-1.23.1-1  libnl-3.2.29-2  libpcap-1.8.1-2  libpciaccess-0.13.5-1  libpng-1.6.29-1
	       libpsl-0.17.0-2	librsvg-2:2.40.17-1  libsasl-2.1.26-11	libseccomp-2.3.2-1  libsecret-0.18.5+14+g9980655-1  libssh2-1.8.0-2  libsystemd-232-8  libtasn1-4.12-1	libtiff-4.0.8-1	 libtirpc-1.0.1-3  libunwind-1.2-1
	       libutil-linux-2.29.2-2  libwacom-0.24-1	libwbclient-4.6.5-1  libx11-1.6.5-1  libxkbcommon-0.7.1-1  libxml2-2.9.4+16+g07418011-2	 licenses-20140629-2  linux-api-headers-4.10.1-1  linux-firmware-20170422.ade8332-1
	       linux-raspberrypi-4.9.31-2  llvm-libs-4.0.0-3  lm_sensors-3.4.0-2  logrotate-3.12.2-1  lvm2-2.02.171-1  lxappearance-0.6.3-1  lxdm-0.5.3-4  lxlauncher-0.2.5-2  lxtask-0.1.8-1  lynx-2.8.8-5  lzo-2.10-1
	       man-pages-4.11-1	 mdadm-4.0-1  mesa-17.1.2-1  mesa-libgl-13.0.3-1 [removal]  mkinitcpio-23-1.1  mkinitcpio-busybox-1.25.1-1  mlocate-0.26-6  nano-2.8.4-1  ncurses-6.0+20170527-1  npth-1.5-1  nspr-4.15-1
	       ntp-4.2.8.p10-2	openresolv-3.9.0-1  openssh-7.5p1-2  openssl-1.1.0.f-1	p11-kit-0.23.7-1  pacman-5.0.1-5  pacman-mirrorlist-20170512-1	pango-1.40.6+9+g92cc73c8-1  pciutils-3.5.4-1  pcre-8.40-1  perl-5.26.0-1
	       perl-encode-locale-1.05-2  perl-file-listing-6.04-3  perl-html-parser-3.72-3  perl-html-tagset-3.20-5  perl-http-cookies-6.03-2	perl-http-daemon-6.01-3	 perl-http-date-6.02-3	perl-http-message-6.11-3
	       perl-http-negotiate-6.01-3  perl-io-html-1.001-2	 perl-libwww-6.26-2  perl-lwp-mediatypes-6.02-3	 perl-net-http-6.16-1  perl-try-tiny-0.28-2  perl-uri-1.71-2  perl-www-robotrules-6.02-3  presentproto-1.1-1
	       python2-2.7.13-2	 raspberrypi-bootloader-20170613-1  raspberrypi-bootloader-x-20170613-1	 raspberrypi-firmware-20170613-1  readline-7.0.003-1  s-nail-14.8.16-2	sed-4.4-1  shared-mime-info-1.8-1
	       smbclient-4.6.5-1  sqlite-3.19.3-1  sshfs-2.9-1	startup-notification-0.12-5  sudo-1.8.20.p2-1  systemd-232-8  systemd-sysvcompat-232-8	talloc-2.1.9-1	tcsh-6.20.00-1	texinfo-6.3-2
	       thin-provisioning-tools-0.7.0-1	tzdata-2017b-1	util-linux-2.29.2-2  vim-runtime-8.0.0628-1  vte-common-0.48.3-1  wayland-1.13.0-1  wayland-protocols-1.7-1  wpa_supplicant-1:2.6-6  xf86-input-libinput-0.25.1-1
	       xfsprogs-4.11.0-1  xkeyboard-config-2.21-1  xmms2-0.8DrO_o.949.gca15e830-2  xorg-mkfontdir-1.0.7-8  xorg-server-1.19.3-2	 xorg-server-common-1.19.3-2  xorg-server-devel-1.19.3-2  xorg-server-xdmx-1.19.3-2
	       xorg-server-xephyr-1.19.3-2  xorg-server-xnest-1.19.3-2	xorg-server-xvfb-1.19.3-2  xorg-server-xwayland-1.19.3-2  xorg-sessreg-1.1.1-1	xorg-util-macros-1.19.1-1  xorg-xauth-1.0.10-1	xorg-xdriinfo-1.0.5-2
	       xorg-xkbcomp-1.4.0-1  xterm-329-1

Total Installed Size:  1137.55 MiB
Net Upgrade Size:	165.21 MiB

:: Proceed with installation? [Y/n]
(195/195) checking keys in keyring													 [####################################################################################] 100%
(195/195) checking package integrity													 [####################################################################################] 100%
(195/195) loading package files														 [####################################################################################] 100%
(195/195) checking for file conflicts													 [####################################################################################] 100%
error: failed to commit transaction (conflicting files)
ca-certificates-utils: /etc/ssl/certs/ca-certificates.crt exists in filesystem
Errors occurred, no packages were upgraded.
[root@alarmpi Progs]# exit

Script done on Wed Jun 14 04:08:11 2017
I've run this several times - always get error. Note that earlier runs downloaded the files OK, then err'd out (always with same message). This run didn't need to download the files, but still crashed with error.

How to fix???

Edit: Solved. Nice to see the system working. Exactly one response to the thread and it contained the answer. Well done!
Last edited by Martin Frezman on Wed Jun 14, 2017 1:43 pm, edited 1 time in total.
If this post appears in the wrong forums category, my apologies.

User avatar
PeterO
Posts: 3632
Joined: Sun Jul 22, 2012 4:14 pm

Re: Cannot update system (error about conflicting files)

Wed Jun 14, 2017 8:29 am

Did you even try to find a solution, or are you just being lazy ?
http://bfy.tw/CMJP
PeterO
Discoverer of the PI2 XENON DEATH FLASH!
Interests: C,Python,PIC,Electronics,Ham Radio (G0DZB),Aeromodelling,1960s British Computers.
"The primary requirement (as we've always seen in your examples) is that the code is readable. " Dougie Lawson

Koeshi
Posts: 224
Joined: Sun Mar 20, 2016 11:16 am

Re: Cannot update system (error about conflicting files)

Wed Jun 14, 2017 11:50 am

Assuming that is the same as on x86 you will need to download the new certificates without installing them, remove the old ones and then install the new ones. There is a post about it here: https://www.archlinux.org/news/ca-certi ... ervention/

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