I'm trying to update to xorg 6.8.2, and the migration step after compilation fails. The logs in /var/log/portage end: <lots of "removed xxx" lines> ... * Symlinking //usr/X11R6/bin -> ../bin * Migrating from /usr/X11R6/include to /usr/include... * Migration method is rsync. * /usr/X11R6/include isn't a symlink, migrating... * rsync successful! removed `//usr/X11R6/include/GL/glut.h' ... <lots of "removed xxx" lines> ... removed `//usr/X11R6/include/images/k4.pr' removed `//usr/X11R ... and then it just stops, mid-line. A re-emerge resulted in: ... QA Notice: /usr/bin/Xorg is setXid, dynamically linked and using lazy bindings. This combination is generally discouraged. Try: CFLAGS='-Wl,-z,now' emerge xorg-x11 >>> Completed installing xorg-x11-6.8.2-r1 into /usr/tmp/portage/xorg-x11-6.8.2-r1/image/ * Migrating from /usr/X11R6/bin to /usr/bin... * Migration method is rsync. * /usr/X11R6/bin is a symlink, not migrating * Migrating from /usr/X11R6/include to /usr/include... * Migration method is rsync. * /usr/X11R6/include is a symlink, not migrating * Migrating from /usr/X11R6/lib to /usr/lib... * Migration method is rsync. * /usr/X11R6/lib isn't a symlink, migrating... ... with no further output. The corresponding files in /usr/tmp/portage/xorg-x11-6.8.2-r1/temp/migrate--*.log read: [First merge] building file list ... 0 files...^M33 files to consider ./ delete_file: rmdir "/usr/lib/X11" failed: Directory not empty symlink "/usr/lib/X11" -> "../../lib/X11" failed: File exists help/ lesstif/ modules/ modules/input/ Number of files: 33 Number of files transferred: 0 Total file size: 1561505 bytes Total transferred file size: 0 bytes Literal data: 0 bytes Matched data: 0 bytes File list size: 873 Total bytes written: 885 Total bytes read: 20 wrote 885 bytes read 20 bytes 603.33 bytes/sec total size is 1561505 speedup is 1725.42 rsync error: some files could not be transferred (code 23) at main.c(632) [Second merge] building file list ... 0 files...^M33 files to consider delete_file: rmdir "/usr/lib/X11" failed: Directory not empty symlink "/usr/lib/X11" -> "../../lib/X11" failed: File exists Number of files: 33 Number of files transferred: 0 Total file size: 1561505 bytes Total transferred file size: 0 bytes Literal data: 0 bytes Matched data: 0 bytes File list size: 873 Total bytes written: 885 Total bytes read: 20 wrote 885 bytes read 20 bytes 1810.00 bytes/sec total size is 1561505 speedup is 1725.42 rsync error: some files could not be transferred (code 23) at main.c(632) ... and finally, the contents of /usr/lib/X11/ are currently (after the 2nd failed merge): total 204K -r--r--r-- 1 root root 2.7K Dec 20 04:24 AuErrorDB -r--r--r-- 1 root root 58K Mar 11 12:59 Cards -r--r--r-- 1 root root 13K Mar 11 12:59 Options -r--r--r-- 1 root root 36K Mar 11 12:59 XErrorDB -r--r--r-- 1 root root 8.2K Mar 11 12:59 XKeysymDB lrwxrwxrwx 1 root root 29 Jul 8 2004 XftConfig -> ../../../../etc/X11/XftConfig lrwxrwxrwx 1 root root 29 Mar 11 12:59 app-defaults -> ../../../etc/X11/app-defaults drwxr-xr-x 2 root root 4.0K Nov 18 20:41 config drwxr-xr-x 2 root root 4.0K Nov 18 02:36 etc drwxr-xr-x 2 root root 4.0K Mar 11 13:02 fonts lrwxrwxrwx 1 root root 19 Mar 11 12:59 fs -> ../../../etc/X11/fs drwxr-xr-x 2 root root 4.0K Nov 18 02:36 getconfig drwxr-xr-x 2 root root 4.0K Sep 8 2004 gv lrwxrwxrwx 1 root root 25 Mar 11 13:00 lbxproxy -> ../../../etc/X11/lbxproxy drwxr-xr-x 55 root root 4.0K Nov 18 02:36 locale drwxr-xr-x 2 root root 4.0K Oct 8 09:51 mwm lrwxrwxrwx 1 root root 26 Mar 11 12:59 proxymngr -> ../../../etc/X11/proxymngr -r--r--r-- 1 root root 17K Mar 11 12:59 rgb.txt lrwxrwxrwx 1 root root 23 Mar 11 12:59 rstart -> ../../../etc/X11/rstart lrwxrwxrwx 1 root root 20 Mar 11 12:59 twm -> ../../../etc/X11/twm drwxr-xr-x 2 root root 4.0K Nov 18 02:36 x11perfcomp lrwxrwxrwx 1 root root 20 Mar 11 12:59 xdm -> ../../../etc/X11/xdm drwxr-xr-x 3 root root 4.0K Oct 26 00:38 xedit lrwxrwxrwx 1 root root 22 Mar 11 12:59 xinit -> ../../../etc/X11/xinit drwxr-xr-x 10 root root 4.0K Mar 11 13:29 xkb -r--r--r-- 1 root root 8.2K Mar 11 12:59 xman.help lrwxrwxrwx 1 root root 24 Mar 11 13:00 xserver -> ../../../etc/X11/xserver lrwxrwxrwx 1 root root 20 Mar 11 13:00 xsm -> ../../../etc/X11/xsm Packages owning these files: /usr/lib/X11/: sys-apps/baselayout-1.9.4-r6 x11-base/xorg-x11-6.8.0-r5 x11-libs/openmotif-2.2.3-r3 x11-libs/lesstif-0.94.0-r2 /usr/lib/X11/config: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/app-defaults: x11-base/xorg-x11-6.8.0-r5 x11-libs/lesstif-0.94.0-r2 /usr/lib/X11/XErrorDB: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/proxymngr: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/rstart: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/locale: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/twm: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xkb: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xdm: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/x11perfcomp: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/XKeysymDB: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/fs: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xsm: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/rgb.txt: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xinit: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xserver: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/etc: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xedit: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/getconfig: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/xman.help: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/lbxproxy: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/Options: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/Cards: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/XftConfig: file /usr/lib/X11/XftConfig is not owned by any package /usr/lib/X11/AuErrorDB: file /usr/lib/X11/AuErrorDB is not owned by any package /usr/lib/X11/fonts: x11-base/xorg-x11-6.8.0-r5 /usr/lib/X11/gv: file /usr/lib/X11/gv is not owned by any package /usr/lib/X11/mwm: x11-libs/lesstif-0.94.0-r2 emerge info: Portage 2.0.51.19 (default-linux/x86/2004.3, gcc-3.3.5, glibc-2.3.4.20040808-r1, 2.6.10-gentoo-r6 i686) ================================================================= System uname: 2.6.10-gentoo-r6 i686 Intel(R) Pentium(R) M processor 1700MHz Gentoo Base System version 1.4.16 Python: dev-lang/python-2.2.3-r6,dev-lang/python-2.3.4-r1 [2.3.4 (#1, Feb 7 2005, 10:05:03)] distcc 2.16 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] dev-lang/python: 2.2.3-r6, 2.3.4-r1 sys-devel/autoconf: 2.59-r6, 2.13 sys-devel/automake: 1.5, 1.7.9-r1, 1.6.3, 1.4_p6, 1.9.4, 1.8.5-r3 sys-devel/binutils: 2.15.92.0.2-r1 sys-devel/libtool: 1.5.10-r4 virtual/os-headers: 2.6.8.1-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CFLAGS="-O2 -march=pentium4 -mfpmath=sse -msse2 -fprefetch-loop-arrays -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/X11/xkb /etc/gconf /etc/env.d" CXXFLAGS="-O2 -march=pentium4 -mfpmath=sse -msse2 -fprefetch-loop-arrays -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig ccache distlocks fixpackages sandbox sfperms userpriv usersandbox" GENTOO_MIRRORS=" http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo http://www.mirror.ac.uk/sites/www.ibiblio.org/gentoo http://ftp.heanet.ie/pub/gentoo http://gentoo.osuosl.org http://gentoo.oregonstate.edu " MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/usr/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.uk.gentoo.org/gentoo-portage" USE="x86 X Xaw3d a52 aac aalib accessibility acl acpi adns alsa arts audiofile avi bash-completion berkdb bitmap-fonts bluetooth bonobo caps cdr crypt cscope cups curl dedicated dga directfb divx4linux dv dvd dvdread eds emboss encode esd ethereal evo fam fastcgi fbcon fftw firebird flac flash font-server foomaticdb fortran freetds freetype gb gcj gd gdbm ggi gif glut gnome gnomedb gnutls gphoto2 gpm gstreamer gtk gtk2 gtkhtml guile hal howl icc-pgo imagemagick imap imlib informix innodb ipv6 jack java javamail javascript joystick jpeg junit kde kdeenablefinal kerberos krb4 ladcca lcms ldap libcaca libg++ libgda libwww lua lzo mad maildir mailwrapper matroska mbox mcal memlimit mikmod milter mmap mmx mng mono motif mozilla mp3 mpeg mpi mssql multislot mysql nas ncurses net network nls nntp nptl oci8 odbc oggvorbis openal opengl oss pam pcmcia pcre pdflib perl pic plotutils png pnp portaudio postgres ppds prelude python qdbm qt quicktime readline real samba sasl scanner sdl skey slang slp sndfile snmp socks5 speex spell sqlite sse sse2 ssl svg svga tcltk tcpd theora tiff truetype truetype-fonts type1-fonts unicode usb v4l v4l2 wmf wxwindows xanim xface xim xine xinerama xml xml2 xmms xosd xprint xv xvid zeo zlib video_cards_radeon" Unset: ASFLAGS, CBUILD, CTARGET, LANG, LC_ALL, LDFLAGS This problem is preventing me from upgrading to xorg-x11-6.8.2-r1, and my X11R6 directory structure is now half-migrated. Thanks!
ls -l /usr/lib* /usr/lib/X11
Okay, I've actually managed to fix this just now... /usr/X11R6/lib/X11 was a link to /usr/lib/X11. I'm not sure why this fixed things, but removing this symlink then allowed the merge to complete successfully. (Of course, removing this may have broken the migration completely - but it looks okay so far) Incidentally, I tried using the "tar" and "mv" migration methods too, and with that symlink in place these all failed too. I still have logs for these, if they'd be useful to attach? Is /usr/X11R6/lib/X11 supposed to be a symlink to /usr/lib/X11?
It's not on my clean install of X.Org 6.8.2-r1. Donnie, this seems very similar to http://bugs.gentoo.org/show_bug.cgi?id=85066
Nah, not really that similar. I elaborated on the other bug. I'm not sure where that symlink came from. If I can track down a valid reason for it to exist (i.e., it wasn't added manually to work around some problem), I'll add a check for it.
I ran through the ebuilds and couldn't find any reference to the creation of this symlink. It's still possible that some previous ebuild could have created it though. Stuart, when did you initially install this current copy of Gentoo on your system? IE, have you been updating the same install for a year or more/less?
Oh, yeah... This machine has was originally installed with Gentoo 1.4 over a year ago (probably coming up to 20 months or so ago, to be honest), so it could well be due to some *ancient* version which few people will have used... I don't remember manually creating this symlink - and while it's not impossible that I did this, I'm 99% sure it wasn't me. Perhaps a one-liner to check whether any entries expected to be directories are actually symlinks could act as a sanity check before migrating settings?
That's related to bug #85710, so perhaps we should make this a duplicate of that.
But in this case we want to remove the symlink instead of keep it. Unless you're thinking both cases would be covered by the same symlink checker?
The general idea would be checking both existence of and validity of symlinks, so I think this falls under that.
Stuart, when you say: <quote> * Migration method is rsync. * /usr/X11R6/lib isn't a symlink, migrating... ... with no further output. </quote> How long did you leave it?
It's been a while now, but IIRC then after outputting "* /usr/X11R6/lib isn't a symlink, migrating..." the script aborted, and I was back at the shell prompt. So it's not a case of having killed it whilst it was processing, but instead that the ebuild just quit. (Also note that the logs in /var/log/portage also just stop, sometimes mid-line, as if a buffer hasn't been flushed)
(In reply to comment #2) > Okay, I've actually managed to fix this just now... > > /usr/X11R6/lib/X11 was a link to /usr/lib/X11. I'm not sure why this fixed things, but removing this symlink then allowed the merge to complete successfully. The symlink was also present in my system (initial install: 2004.3, xorg 6.8.0) - it was also causing final merging to fail (trying so symlink /usr/lib/X11 to itself). The emerge finished cleanly after I unlinked it. I can't remember if I created the link, but if I did, it was probably in an attempt to fix some keyboard map errors I had in Gnome back then (using xfce now).
6.8.2 won't be receiving any more non-security changes, and this bug doesn't apply to 7.0.
