libxml2 update problem

[zdn3023]

I was trying to update my system, and got stuck with libxml2. The update went ok for a while but then stoped. I just copied the end of the message. Any good ideas about what went wrong?

... ... gcc -march=i686 -g -pipe -pedantic -W -Wformat -Wunused -Wimplicit -Wreturn-type -Wswitch -Wcomment -Wtrigraphs -Wformat -Wchar-subscripts -Wuninitialized -Wparentheses -Wshadow -Wpointer-arith -Wcast-align -Wwrite-strings -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wnested-externs -Winline -Wredundant-decls -o .libs/xmllint xmllint.o ./.libs/libxml2.so -ldl -lz -lm
./.libs/libxml2.so: undefined reference to `pthread_getspecific'
./.libs/libxml2.so: undefined reference to `pthread_once'
./.libs/libxml2.so: undefined reference to `pthread_key_create'
./.libs/libxml2.so: undefined reference to `pthread_setspecific'
collect2: ld returned 1 exit status
make[2]: *** [xmllint] Error 1
make[2]: Leaving directory `/var/tmp/portage/libxml2-2.6.20-r2/work/libxml2-2.6.20'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/var/tmp/portage/libxml2-2.6.20-r2/work/libxml2-2.6.20'
make: *** [all] Error 2

!!! ERROR: dev-libs/libxml2-2.6.20-r2 failed.
!!! Function src_compile, Line 58, Exitcode 2
!!! Copilation failed
!!! If you need support, post the topmost build error, NOT this status message.
[/code]
Thank you in advance if you have any suggestions!

[yabbadabbadont]

Post the contents of /etc/make.conf and the output of 'emerge --info'.

[zdn3023]

/etc/make.conf

# Copyright 2000-2003 Daniel Robbins, Gentoo Technologies, Inc.
# Contains local system settings for Portage system
# $Header: /home/cvsroot/gentoo-src/portage/cnf/make.conf,v 1.57 2003/03/11 11:33:07 carpaski Exp $

# Please review 'man make.conf' for more information.

# Build-time functionality
# ========================
#
# The USE variable is used to enable optional build-time functionality. For
# example, quite a few packages have optional X, gtk or GNOME functionality
# that can only be enabled or disabled at compile-time. Gentoo Linux has a
# very extensive set of USE variables described in our USE variable HOWTO at
# http://www.gentoo.org/doc/use-howto.html
#
# The available list of use flags with descriptions is in your portage tree.
# Use 'less' to view them: --> less /usr/portage/profiles/use.desc <--
#
# 'ufed' is an ncurses/dialog interface available in portage to make handling
# useflags for you. 'emerge app-admin/ufed'
#
# Example:
#USE="X gtk gnome -alsa"

# Host Setting
# ============
#
# If you are using a Pentium Pro or greater processor, leave this line as-is;
# otherwise, change to i586, i486 or i386 as appropriate. All modern systems
# (even Athlons) should use "i686-pc-linux-gnu"
#
CHOST="i686-pc-linux-gnu"

# Host and optimization settings
# ==============================
#
# For optimal performance, enable a CFLAGS setting appropriate for your CPU.
#
# Please note that if you experience strange issues with a package, it may be
# due to gcc's optimizations interacting in a strange way. Please test the
# package (and in some cases the libraries it uses) at default optimizations
# before reporting errors to developers.
#
# -mcpu=<cpu-type> means optimize code for the particular type of CPU without
# breaking compatibility with other CPUs.
#
# -march=<cpu-type> means to take full advantage of the ABI and instructions
# for the particular CPU; this will break compatibility with older CPUs (for
# example, -march=athlon-xp code will not run on a regular Athlon, and
# -march=i686 code will not run on a Pentium Classic.
#
# CPU types supported in gcc-3.2 and higher: athlon-xp, athlon-mp,
# athlon-tbird, athlon, k6, k6-2, k6-3, i386, i486, i586 (Pentium), i686
# (PentiumPro), pentium, pentium-mmx, pentiumpro, pentium2 (Celeron), pentium3.
# Note that Gentoo Linux 1.4 and higher include at least gcc-3.2.
# ATHLON-4 will generate invalid SSE instructions; use 'athlon' instead.
# PENTIUM4 will generate invalid instructions; use 'pentium3' instead.
#
# CPU types supported in gcc-2.95*: k6, i386, i486, i586 (Pentium), i686
# (Pentium Pro), pentium, pentiumpro Gentoo Linux 1.2 and below use gcc-2.95*
#
# Decent examples:
#
#CFLAGS="-mcpu=athlon-xp -O3 -pipe"
#CFLAGS="-march=pentium3 -O3 -pipe"
CFLAGS="-march=i686 -g -pipe"

# If you set a CFLAGS above, then this line will set your default C++ flags to
# the same settings.
#CXXFLAGS="${CFLAGS}"
CXXFLAGS="${CFLAGS}"

# Advanced Masking
# ================
#
# Gentoo is using a new masking system to allow for easier stability testing
# on packages. KEYWORDS are used in ebuilds to mask and unmask packages based
# on the platform they are set for. A special form has been added that
# indicates packages and revisions that are expected to work, but have not yet
# been approved for the stable set. '~arch' is a superset of 'arch' which
# includes the unstable, in testing, packages. Users of the 'x86' architecture
# would add '~x86' to ACCEPT_KEYWORDS to enable unstable/testing packages.
# '~ppc', '~sparc', '~sparc64' are the unstable KEYWORDS for their respective
# platforms. DO NOT PUT ANYTHING BUT YOUR SPECIFIC ~ARCHITECTURE IN THE LIST.
# IF YOU ARE UNSURE OF YOUR ARCH, OR THE IMPLICATIONS, DO NOT MODIFY THIS.
#
#ACCEPT_KEYWORDS="~arch"

# Portage Directories
# ===================
#
# Each of these settings controls an aspect of portage's storage and file
# system usage. If you change any of these, be sure it is available when
# you try to use portage. *** DO NOT INCLUDE A TRAILING "/" ***
#
# PORTAGE_TMPDIR is the location portage will use for compilations and
# temporary storage of data. This can get VERY large depending upon
# the application being installed.
#PORTAGE_TMPDIR=/var/tmp
#
# PORTDIR is the location of the portage tree. This is the repository
# for all profile information as well as all ebuilds. This directory
# itself can reach 200M. WE DO NOT RECOMMEND that you change this.
#PORTDIR=/usr/portage
#
# DISTDIR is where all of the source code tarballs will be placed for
# emerges. The source code is maintained here unless you delete
# it. The entire repository of tarballs for gentoo is 9G. This is
# considerably more than any user will ever download. 2-3G is
# a large DISTDIR.
#DISTDIR=${PORTDIR}/distfiles
#
# PKGDIR is the location of binary packages that you can have created
# with '--buildpkg' or '-b' while emerging a package. This can get
# upto several hundred megs, or even a few gigs.
#PKGDIR=${PORTDIR}/packages
#
# PORT_LOGDIR is the location where portage will store all the logs it
# creates from each individual merge. They are stored as YYMMDD-$PF.log
# in the directory specified. This is disabled until you enable it by
# providing a directory. Permissions will be modified as needed IF the
# directory exists, otherwise logging will be disabled.
#PORT_LOGDIR=/var/log/portage
#
# PORTDIR_OVERLAY is a directory where local ebuilds may be stored without
# concern that they will be deleted by rsync updates. Default is not
# defined.
#PORTDIR_OVERLAY=/usr/local/portage

# Fetching files
# ==============
#
# If you need to set a proxy for wget or lukemftp, add the appropriate "export
# ftp_proxy=<proxy>" and "export http_proxy=<proxy>" lines to /etc/profile if
# all users on your system should use them.
#
# Portage uses wget by default. Here are some settings for some alternate
# downloaders -- note that you need to merge these programs first before they
# will be available.
#
# Default fetch command (5 tries, passive ftp for firewall compatibility)
#FETCHCOMMAND="/usr/bin/wget -t 5 --passive-ftp \${URI} -P \${DISTDIR}"
#RESUMECOMMAND="/usr/bin/wget -c -t 5 --passive-ftp \${URI} -P \${DISTDIR}"
#
# Using wget, ratelimiting downloads
#FETCHCOMMAND="/usr/bin/wget -t 5 --passive-ftp --limit-rate=200k \${URI} -P \${DISTDIR}"
#RESUMECOMMAND="/usr/bin/wget -c -t 5 --passive-ftp --limit-rate=200k \${URI} -P \${DISTDIR}"
#
# Lukemftp (BSD ftp):
#FETCHCOMMAND="/usr/bin/lukemftp -s -a -o \${DISTDIR}/\${FILE} \${URI}"
#RESUMECOMMAND="/usr/bin/lukemftp -s -a -R -o \${DISTDIR}/\${FILE} \${URI}"
#
# Prozilla (turbo downloader)
#FETCHCOMMAND='/usr/bin/proz --no-getch -s ${URI} -P ${DISTDIR}'
#
# Portage uses GENTOO_MIRRORS to specify mirrors to use for source retrieval.
# The list is a space seperated list which is read left to right. If you use
# another mirror we highly recommend leaving the default mirror at the end of
# the list so that portage will fall back to it if the files cannot be found
# on your specified mirror. We _HIGHLY_ recommend that you change this setting
# to a nearby mirror by merging and using the 'mirrorselect' tool.
#GENTOO_MIRRORS="<your_mirror_here> http://gentoo.oregonstate.edu/ http://www.ibiblio.org/pub/Linux/distributions/gentoo"

# Advanced Features
# =================
#
# MAKEOPTS provides extra options that may be passed to 'make' when a
# program is compiled. Presently the only use is for specifying
# the number of parallel makes (-j) to perform. The suggested number
# for parallel makes is CPUs+1.
#MAKEOPTS="-j2"
#
# AUTOCLEAN enables portage to automatically clean out older or overlapping
# packages from the system after every successful merge. This is the
# same as running 'emerge -c' after every merge. Set with: "yes" or "no".
# This does not affect the unpacked source. See 'noclean' below.
#AUTOCLEAN="yes"
#
# FEATURES are settings that affect the functionality of portage. Most of
# these settings are for developer use, but some are available to non-
# developers as well. 'buildpkg' is an always-on setting for the emerge
# flag of the same name. It causes binary packages to be created of all
# packages that are merged. 'distcc' enables distcc support for via CC.
# 'userpriv' allows portage to drop root privleges while it is compiling
# as a security measure, and as a side effect this can remove sandbox
# access violations for users. 'usersandbox' enables sandboxing while
# portage is running under userpriv. 'noclean' prevents portage from
# removing the source and temporary files after a merge -- for debugging
# purposes only. 'noauto' is a feature which causes ebuild to perform
# the action requested and not any other required actions like clean or
# unpack -- for debugging purposes only. 'cvs' is a feature for developers
# that causes portage to enable full settings and USE flags in SRC_URI and
# has wide effects -- don't set this unless you're ready for it. 'keeptemp'
# prevents the clean phase from deleting the temp files ($T) from a merge.
# 'keepwork' prevents the clean phase from deleting the $WORKDIR.
FEATURES="sandbox buildpkg ccache distcc userpriv usersandbox noclean noauto cvs keeptemp keepwork nostrip"
#
# CCACHE_SIZE sets the space use limitations for ccache. The default size is
# 2G, and will be set if not defined otherwise and ccache is in features.
# Portage will set the default ccache dir if it is not present in the
# user's environment: ${PORTAGE_TMPDIR}/ccache (/var/tmp/ccache).
# Sizes are specified with 'G' 'M' or 'K'.
# '4G' for 4 gigabytes, '4096M' for 4 gigabytes, etc... Default is 2G
#CCACHE_SIZE="2G"
#
# RSYNC_RETRIES sets the number of times portage will attempt to retrieve
# a current portage tree before it exits with an error. This allows
# for a more successful retrieval without user intervention most times.
#RSYNC_RETRIES="3"
#
# RSYNC_TIMEOUT sets the length of time rsync will wait before it times out
# on a connection. Most users will benefit from this setting as it will
# reduce the amount of 'dead air' they experience when they run across
# the occasional, unreachable mirror. Dialup users might want to set this
# value up around the 300 second mark.
#RSYNC_TIMEOUT=180
#
# RSYNC_EXCLUDEFROM is a file that portage will pass to rsync when it updates
# the portage tree. Specific chucks of the tree may be excluded from
# consideration. This may cause dependency failures if you are not careful.
# The file format is one pattern per line, blanks and ';' or '#' lines are
# comments. See 'man rsync' for more details on the exclude-from format.
#RSYNC_EXCLUDEFROM=/etc/portage/rsync_excludes

emerge --info
Portage 2.0.51.22-r3 (default-linux/x86/2005.0/2.4, gcc-3.2.3, glibc-2.3.5-r2, 2.4.20-gentoo-r5 i686)
=================================================================
System uname: 2.4.20-gentoo-r5 i686 Intel(R) Pentium(R) 4 CPU 2.80GHz
Gentoo Base System version 1.4.3.8p1
dev-lang/python: 2.2.3-r1
sys-apps/sandbox: 1.2.12
sys-devel/autoconf: 2.13, 2.59-r6
sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1
sys-devel/binutils: 2.14.90.0.6-r2
sys-devel/libtool: 1.4.3-r1
virtual/os-headers: 2.4.19-r1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=i686 -g -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/X11R6/lib/X11/xkb /usr/kde/2/share/config /usr/kde/3.1/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d"
CXXFLAGS="-march=i686 -g -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig buildpkg ccache cvs distcc distlocks keeptemp keepwork noauto noclean nostrip sandbox sfperms strict userpriv usersandbox"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X alsa apm arts avi berkdb bitmap-fonts crypt cscope cups curl eds emboss encode esd fam foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 imlib ipv6 java jpeg kde libg++ libwww mad mikmod motif mozilla mp3 mpeg ncurses nls ogg oggvorbis opengl oss pam pdflib perl png python qt quicktime readline samba sdl slang spell ssl svga tcltk tcpd tiff truetype truetype-fonts type1-fonts vorbis xml xml2 xmms xv zlib userland_GNU kernel_linux elibc_glibc"
Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTDIR_OVERLAY

[yabbadabbadont]

Try enabling the 'threads' USE flag and then emerge libxml2 again. I don't know if this will fix it, but it is complaining about pthreads and the use.desc file says: "threads - Adds threads support for various packages. Usually pthreads"

If that does work, then I don't know why the libxml2 ebuild doesn't list 'threads' as one of it's USE flags.

[Aziere]

I had this very same problem. And using the "threads" USE-flag made it function correctly. Thanks yabbadabbadont.