Part way through emerging kdelibs, I get "undefined symbol" errors as below. I've tried re-emerging both zlib and libxml2, and get the same results still. [ 65%] Generating index.cache.bz2 /usr/bin/xmllint: symbol lookup error: /usr/lib/libxml2.so.2: undefined symbol: gzdirect make[2]: *** [doc/kioslave/data/index.cache.bz2] Error 1 Reproducible: Always Steps to Reproduce: 1. emerge kdelibs 2. 3. Actual Results: kdelibs not merged. Expected Results: kdelibs merged. [21:49] enigmas zlib # emerge --info Portage 2.1.8.3 (default/linux/x86/10.0, gcc-4.4.3, glibc-2.11.2-r0, 2.6.34-gentoo-r1 i686) ================================================================= System uname: Linux-2.6.34-gentoo-r1-i686-Intel-R-_Core-TM-2_Duo_CPU_E8200_@_2.66GHz-with-gentoo-1.12.13 Timestamp of tree: Sun, 10 Oct 2010 08:30:21 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11 dev-lang/python: 2.6.5-r3, 3.1.2-r4 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 2.3-r1 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.9.6-r2, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.3.4, 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA Q3AEULA dlj-1.1 AdobeFlash-10.1" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=prescott -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=prescott -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests ccache distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://ftp.iinet.net.au/linux/Gentoo http://ftp.swin.edu.au/gentoo" LANG="en_AU.UTF-8" LC_ALL="en_AU.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/layman/sunrise /usr/local/portage/layman/rion /usr/local/portage/layman/glc /usr/local/portage/layman/mt-mythtv /usr/local/portage/layman/science /usr/local/portage/layman/unknown-horizons /usr/local/portage" SYNC="rsync://games/gentoo-portage" USE="3dnow 3dnowex 3dnowext X a52 aac aalib acl acpi aim alsa asf avi berkdb bzip bzip2 cairo cdr cli consolekit cracklib crypt cups curl cxx dbus dga divx dri dts dvd dvdr dvdread encode ethereal evo f77 ffmpeg fftw flac flash foomaticdb fortran ftp gdbm gif glut glx gnome gnutls gpm gtk gtk2 iconv icq imagemagick ipv6 ithreads jabber java java5 java6 joystick jpeg lcms libcaca lirc mad mjpeg mmx mmx2 mmxext modules mozilla mp3 mpeg mplayer msn mudflap mysql mythtv ncurses nls nptl nptlonly nsplugin nvidia offensive ogg oggvorbis openal opengl openmp pam pcre pdf pdflib perl png ppds pppd python qt3support quicktime rar readline reflection samba sdl sensord session sse sse2 ssl subversion svg sysfs szip tcpd theora threads tiff tk truetype truetype-fonts type1-fonts unicode usb vdpau videos vim-syntax vorbis webdav x264 x86 xinerama xml xorg xprint xulrunner xv xvid xvmc yahoo zlib" ALSA_CARDS="hda-intel cs46xx" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php-5.2" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Check your system that it doesn't have zlib.h or zconf.h in some 'odd' directory, like /usr/local/include, like e.g.: find /usr -name zlib.h Then post output of: emerge -pv zlib libxml2
Those files can be found in /usr/include, or under /usr/portage/distfiles/svn-src/xbmc, or in /usr/src/linux-2.6.34 and .35 kernel sources Full listing at http://dpaste.org/wA6d/ [06:38] enigmas ~ # emerge -pv zlib libxml2 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sys-libs/zlib-1.2.3-r1 0 kB [ebuild R ] dev-libs/libxml2-2.7.7 USE="ipv6 python readline -debug -doc -examples -test" 0 kB Total: 2 packages (2 reinstalls), Size of downloads: 0 kB * IMPORTANT: 3 news items need reading for repository 'gentoo'. * Use eselect news to read news items.
full build.log plz
Full build.log is available at http://www.strudel-hound.com/build.log
(Please use bugzilla attachments next time instead of third-party services) Did you try to rebuild libxml2 and revdep-rebuild?
First thing I checked was revdep-rebuild, but it listed nothing broken. I next tried re-emerging libxml2 since that had the issue, but that didn't change anything. After that I re-emerged zlib, and then libxml2, but that still had the same results.
OK, next suggestion- emerge lafilefixer, run lafilefixer --justfixit and then try again revdep-rebuild and afterwards emerge kdelibs... Let us know if that helps!
Ran lafilefixer --justfixit and it did have to fix some .la files. revdep-rebuild did then pull in some new packages, but nothing seemed relevant, the closest was gcc-4.3.4 but I'm running gcc:4.4 in my profile, 4.3 is for CUDA 2.2 development. Ran emerge kdelibs again, still got the same result, /usr/lib/libxml2.so.2: undefined symbol: gzdirect
Ok, I've finally gotten some time to look into this. The file that is failing the symbol is not "/usr/bin/xmllint". After digging through makefiles, it seems KDE uses an internal version of xmllint, called "/var/tmp/portage/kde-base/kdelibs-4.4.5/work/kdelibs-4.4.5_build/bin/meinproc4", and called from a shell script which sets up LD_LIBRARY_PATH. Anyway, that finally pointed out my problem. I somehow had remnants of libz-1.1.4 sitting in /usr/lib/ (/usr/lib/libz.so.1{,.1.4} to be exact). With the changed LD_LIBRARY_PATH, somehow meinproc4 was pulling in /usr/lib/libz.so.1 which is where the symbol was missing from, rather than pulling in /lib/libz.so which did have the symbol. So removed, my extra libraries (well, temporarily moved them until I know for sure everything still works) but kdelibs now emerges fine, so this bug can be closed.
Thank you!
