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Old 10-04-2010, 01:49 PM
Antoine Dechaume
 
Default libxml2 + zlib problem ?

Hi,

I am not sure this problem is related to gentoo, sorry about that if
it happens to be unrelated...


I have a C++ code linked to libxml2, and used through a python
wrapper, whenever I try to load the python module I get:
ImportError: /space/dechaume/prefix/usr/lib/libxml2.so.2: symbol
gzopen64, version ZLIB_1.2.3.3 not defined in file libz.so.1 with link
time reference


I don't know how to interpret this message :-/

Here are some informations:

> emerge --info libxml2
Portage 2.2.01.15553-prefix (prefix/linux/amd64, gcc-4.2.4,
unavailable, 2.6.30.10-105.2.23.fc11.x86_64 x86_64)

================================================== ===============
System Settings
================================================== ===============
System uname: Linux-2.6.30.10-105.2.23.fc11.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5530_@_2.40GHz-with-fedora-11-Leonidas
Timestamp of tree: Sun, 03 Oct 2010 21:41:20 +0000
ccache version 2.4 [disabled]
app-shells/bash: 4.1_p7
dev-lang/python: 2.6.5-r2
sys-devel/autoconf: 2.65-r1
sys-devel/automake: 1.11.1
sys-devel/binutils: 2.20.51.0.10
sys-devel/gcc: 4.2.4-r01.2, 4.4.4-r1
sys-devel/gcc-config: 1.4.1-r00.2
sys-devel/libtool: 2.2.10
sys-devel/make: 3.81-r2
virtual/os-headers: 2.6.35 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="~amd64-linux"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /
etc/revdep-rebuild /etc/terminfo"

CXXFLAGS="-O2 -pipe -march=native"
DISTDIR="/space/dechaume/prefix/usr/portage/distfiles"
FEATURES="assume-digests collision-protect distlocks fixlafiles
fixpackages news parallel-fetch preserve-libs protect-owned sfperms
strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"

GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j8"
PKGDIR="/space/dechaume/prefix/usr/portage/packages"
PORTAGE_CONFIGROOT="/space/dechaume/prefix/"
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="/space/dechaume/prefix/var/tmp"
PORTDIR="/space/dechaume/prefix/usr/portage"
PORTDIR_OVERLAY="/space/dechaume/gentoo/overlay"
SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix"
USE="amd64 bzip2 cxx gdbm iconv ipv6 mmx mudflap ncurses nls nptl
nptlonly openmp pcre perl prefix python readline sse sse2 sse3 ssl
unicode zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x
ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel
intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem
ymfpci" 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" RUBY_TARGETS="ruby18"
USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic
nouveau nv r128 radeon savage sis tdfx trident vesa via vmware voodoo"
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,
LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS,
PORTAGE_RSYNC_EXTRA_OPTS


================================================== ===============
Package Settings
================================================== ===============

dev-libs/libxml2-2.7.7 was built with the following:
USE="ipv6 (prefix) python readline test -debug -doc -examples"


> emerge --info zlib
Portage 2.2.01.15553-prefix (prefix/linux/amd64, gcc-4.2.4,
unavailable, 2.6.30.10-105.2.23.fc11.x86_64 x86_64)

================================================== ===============
System Settings
================================================== ===============
System uname: Linux-2.6.30.10-105.2.23.fc11.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5530_@_2.40GHz-with-fedora-11-Leonidas
Timestamp of tree: Sun, 03 Oct 2010 21:41:20 +0000
ccache version 2.4 [disabled]
app-shells/bash: 4.1_p7
dev-lang/python: 2.6.5-r2
sys-devel/autoconf: 2.65-r1
sys-devel/automake: 1.11.1
sys-devel/binutils: 2.20.51.0.10
sys-devel/gcc: 4.2.4-r01.2, 4.4.4-r1
sys-devel/gcc-config: 1.4.1-r00.2
sys-devel/libtool: 2.2.10
sys-devel/make: 3.81-r2
virtual/os-headers: 2.6.35 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="~amd64-linux"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /
etc/revdep-rebuild /etc/terminfo"

CXXFLAGS="-O2 -pipe -march=native"
DISTDIR="/space/dechaume/prefix/usr/portage/distfiles"
FEATURES="assume-digests collision-protect distlocks fixlafiles
fixpackages news parallel-fetch preserve-libs protect-owned sfperms
strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"

GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j8"
PKGDIR="/space/dechaume/prefix/usr/portage/packages"
PORTAGE_CONFIGROOT="/space/dechaume/prefix/"
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="/space/dechaume/prefix/var/tmp"
PORTDIR="/space/dechaume/prefix/usr/portage"
PORTDIR_OVERLAY="/space/dechaume/gentoo/overlay"
SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix"
USE="amd64 bzip2 cxx gdbm iconv ipv6 mmx mudflap ncurses nls nptl
nptlonly openmp pcre perl prefix python readline sse sse2 sse3 ssl
unicode zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x
ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel
intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem
ymfpci" 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" RUBY_TARGETS="ruby18"
USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic
nouveau nv r128 radeon savage sis tdfx trident vesa via vmware voodoo"
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,
LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS,
PORTAGE_RSYNC_EXTRA_OPTS


================================================== ===============
Package Settings
================================================== ===============

sys-libs/zlib-1.2.5-r2 was built with the following:
USE="(prefix)"
 
Old 10-05-2010, 07:24 AM
Fabian Groffen
 
Default libxml2 + zlib problem ?

On 04-10-2010 15:49:00 +0200, Antoine Dechaume wrote:
> Hi,
>
> I am not sure this problem is related to gentoo, sorry about that if
> it happens to be unrelated...
>
> I have a C++ code linked to libxml2, and used through a python
> wrapper, whenever I try to load the python module I get:
> ImportError: /space/dechaume/prefix/usr/lib/libxml2.so.2: symbol
> gzopen64, version ZLIB_1.2.3.3 not defined in file libz.so.1 with link
> time reference

can you run the following commnds:
% scanelf --needed /space/dechaume/prefix/usr/lib/libxml2.so.2
% scanelf --rpath /space/dechaume/prefix/usr/lib/libxml2.so.2

also try to locate the python module that you include, and run the same
commands on it.


--
Fabian Groffen
Gentoo on a different level
 
Old 10-07-2010, 07:58 AM
Antoine Dechaume
 
Default libxml2 + zlib problem ?

On 5 oct. 10, at 09:24, Fabian Groffen wrote:


On 04-10-2010 15:49:00 +0200, Antoine Dechaume wrote:

Hi,

I am not sure this problem is related to gentoo, sorry about that if
it happens to be unrelated...

I have a C++ code linked to libxml2, and used through a python
wrapper, whenever I try to load the python module I get:
ImportError: /space/dechaume/prefix/usr/lib/libxml2.so.2: symbol
gzopen64, version ZLIB_1.2.3.3 not defined in file libz.so.1 with
link

time reference


can you run the following commnds:
% scanelf --needed /space/dechaume/prefix/usr/lib/libxml2.so.2
% scanelf --rpath /space/dechaume/prefix/usr/lib/libxml2.so.2


> scanelf --needed /space/dechaume/prefix/usr/lib/libxml2.so.2
TYPE NEEDED FILE
ET_DYN libdl.so.2,libz.so.1,libm.so.6,libc.so.6 /space/dechaume/prefix/
usr/lib/libxml2.so.2


> scanelf --rpath /space/dechaume/prefix/usr/lib/libxml2.so.2
TYPE RPATH FILE
ET_DYN /space/dechaume/prefix/usr/x86_64-pc-linux-gnu/lib/gcc:/space/
dechaume/prefix/usr/x86_64-pc-linux-gnu/lib:/space/dechaume/prefix/usr/
lib:/space/dechaume/prefix/lib /space/dechaume/prefix/usr/lib/
libxml2.so.2


also try to locate the python module that you include, and run the
same

commands on it.




> scanelf --needed _FSDataManager.so
TYPE NEEDED FILE
ET_DYN
libFSCommon
.so
,libFSBoundaryCondition
.so
,libFSMesh
.so
,libFSDataLog
.so
,libFSRelationsModel
.so,libFSGeometry.so,libFSDataManager.so,libpthrea d.so.0,libdl.so.
2,libutil.so.1,libpython2.6.so.1.0,libmpi.so.0,lib hdf5_hl.so.
0,libhdf5.so.0,libnetcdf.so.4,libcgns.so.2,libxml2 .so.2,libparmetis.so.
2,libmetis.so.4,libdamas.so,libmutil.so,liberrare. so,libsda.so,libstdc+
+.so.6,libm.so.6,libgcc_s.so.1,libc.so.6 _FSDataManager.so


> scanelf --rpath _FSDataManager.so
TYPE RPATH FILE
ET_DYN /space/dechaume/prefix/usr/x86_64-pc-linux-gnu/lib/gcc:/space/
dechaume/prefix/usr/x86_64-pc-linux-gnu/lib:/space/dechaume/prefix/usr/
lib:/space/dechaume/prefix/lib _FSDataManager.so



Thanks,
Antoine.


--
Fabian Groffen
Gentoo on a different level
 

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