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Bug 448556 - dev-db/sqlite: /usr/lib64/libsqlite3.so: undefined reference to `pthread_mutexattr_settype' (was: net-misc/mediatomb fails to ./configure)
Summary: dev-db/sqlite: /usr/lib64/libsqlite3.so: undefined reference to `pthread_mute...
Status: RESOLVED INVALID
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Arfrever Frehtes Taifersar Arahesis
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2012-12-25 16:25 UTC by Michael Mair-Keimberger (iamnr3)
Modified: 2013-01-21 17:40 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
config.log of mediatomb (r2) (config.log,121.03 KB, text/plain)
2012-12-26 09:06 UTC, Michael Mair-Keimberger (iamnr3)
Details
build log of sqlite (build.log,16.70 KB, text/plain)
2013-01-21 09:09 UTC, Michael Mair-Keimberger (iamnr3)
Details
config.log of sqlite (config.log,56.28 KB, text/plain)
2013-01-21 09:09 UTC, Michael Mair-Keimberger (iamnr3)
Details

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Description Michael Mair-Keimberger (iamnr3) 2012-12-25 16:25:31 UTC
Ive tried to install mediatomb but unfortunately it doesn't work. I've tried the latest stable (r2) plus the latest unstable (r4). both fail at configure sqlite. I've tried to reinstall sqlite and run revdep-rebuild. Below is the build log from the r2 (i deleted a few lines in the middle):

 * Package:    net-misc/mediatomb-0.12.1-r2
 * Repository: gentoo
 * Maintainer: media-video@gentoo.org
 * USE:        amd64 elibc_glibc exif ffmpeg kernel_linux libextractor mp4 taglib thumbnail userland_GNU
 * FEATURES:   sandbox
.
.
.
.
checking for ioctl... yes
checking for tolower... yes
checking for toupper... yes
checking for inet_ntoa... yes
checking for socket... yes
checking for gethostbyname... yes
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for gethostbyname_r... yes
checking for if_nameindex... yes
checking for if_freenameindex... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for clock_gettime in -lrt... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for uncompress in -lz... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for sqlite3_open in -lsqlite3... no
checking for sqlite3_open in -lsqlite3... no
configure: error: unable to configure sqlite3 support

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/net-misc/mediatomb-0.12.1-r2/work/mediatomb-0.12.1/config.log
 * ERROR: net-misc/mediatomb-0.12.1-r2 failed (configure phase):
 *   econf failed
 * 
 * Call stack:
 *          ebuild.sh, line   93:  Called src_configure
 *        environment, line 3571:  Called econf '--disable-tombdebug' '--enable-libexif' '--disable-inotify' '--disable-libjs' '--disable-lastfmlib' '--enable-libmp4v2' '--disable-mysql' '--enable-sqlite3' '--enable-taglib' '--disable-id3lib' '--enable-curl' '--enable-external-transcoding' '--enable-libmagic' '--enable-protocolinfo-extension' '--enable-youtube' '--enable-zlib' '--enable-ffmpegthumbnailer' '--enable-ffmpeg' '--disable-libextractor'
 *   phase-helpers.sh, line  501:  Called die
 * The specific snippet of code:
 *                      die "econf failed"
 * 
 * If you need support, post the output of `emerge --info '=net-misc/mediatomb-0.12.1-r2'`,
 * the complete build log and the output of `emerge -pqv '=net-misc/mediatomb-0.12.1-r2'`.
 * The complete build log is located at '/var/tmp/portage/net-misc/mediatomb-0.12.1-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/net-misc/mediatomb-0.12.1-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/net-misc/mediatomb-0.12.1-r2/work/mediatomb-0.12.1'
 * S: '/var/tmp/portage/net-misc/mediatomb-0.12.1-r2/work/mediatomb-0.12.1'


emerge --info:
Portage 2.1.11.31 (default/linux/amd64/10.0/no-multilib, gcc-4.5.4, glibc-2.15-r3, 3.5.7-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.5.7-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5405_@_2.00GHz-with-gentoo-2.1
Timestamp of tree: Tue, 25 Dec 2012 05:45:01 +0000
ld GNU ld (GNU Binutils) 2.22
app-shells/bash:          4.2_p37
dev-lang/python:          2.7.3-r2, 3.2.3
dev-util/cmake:           2.8.9
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.69
sys-devel/automake:       1.11.6
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.4
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.6 (virtual/os-headers)
sys-libs/glibc:           2.15-r3
Repositories: gentoo x-local x11 sunrise virtualization
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native -fopenmp"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/openvpn/easy-rsa"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=native -fopenmp"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="        http://gentoo.supp.name/                                http://ftp.fi.muni.cz/pub/linux/gentoo/                         http://gentoo.mirror.web4u.cz/                          http://gentoo.mirror.dkm.cz/pub/gentoo/                         http://gentoo.ynet.sk/pub"
LANG="de_DE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -fopenmp"
MAKEOPTS="-j12"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/mnt/data/public/overlays/local /mnt/data/public/overlays/layman/x11 /mnt/data/public/overlays/layman/sunrise /mnt/data/public/overlays/layman/virtualization"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage/"
USE="acl acpi amd64 berkdb bzip2 cli cracklib crypt cups cxx dbus dri fortran gdbm gif gpm iconv ipv6 mmx modules mudflap ncurses nls nptl openmp pam pbm pcre png pppd readline session sqlite sse sse2 ssl ssse3 tcpd threads 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="authn_core authz_core socache_shmcb unixd 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" 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" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="i386 x86_64 mips arm ppc ppc64" QEMU_USER_TARGETS="i386 x86_64 mips arm ppc ppc64" RUBY_TARGETS="ruby18 ruby19" SANE_BACKENDS="niash" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON


sqlite settings:
=================================================================
                        Package Settings
=================================================================

dev-db/sqlite-3.7.14.1 was built with the following:
USE="extensions fts3 readline threadsafe -debug -doc -icu -secure-delete -soundex -tcl -test -unlock-notify"
Comment 1 Jeroen Roovers (RETIRED) gentoo-dev 2012-12-25 17:52:33 UTC
(In reply to comment #0)
> !!! Please attach the following file when seeking support:
> !!!
> /var/tmp/portage/net-misc/mediatomb-0.12.1-r2/work/mediatomb-0.12.1/config.
> log

Please do.
Comment 2 Michael Mair-Keimberger (iamnr3) 2012-12-26 09:06:35 UTC
Created attachment 333370 [details]
config.log of mediatomb (r2)

sorry.. forget to add that.
Comment 3 Ian Whyman (thev00d00) (RETIRED) gentoo-dev 2013-01-20 19:30:29 UTC
Is this still an issue for you?

Which version of sqlite are you using?
Comment 4 Samuli Suominen (RETIRED) gentoo-dev 2013-01-20 21:21:28 UTC
seems like missing -lpthread linking in sqlite, reassigning to sqlite maintainers
Comment 5 Arfrever Frehtes Taifersar Arahesis 2013-01-20 21:28:36 UTC
(In reply to comment #4)
> seems like missing -lpthread linking in sqlite

I cannot reproduce it:
$ readelf -d /usr/lib64/libsqlite3.so | grep libpthread
 0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
$

Reporter of this bug: Please attach build log and config.log of SQLite.
Comment 6 Michael Mair-Keimberger (iamnr3) 2013-01-21 09:09:23 UTC
Created attachment 336320 [details]
build log of sqlite
Comment 7 Michael Mair-Keimberger (iamnr3) 2013-01-21 09:09:42 UTC
Created attachment 336322 [details]
config.log of sqlite
Comment 8 Michael Mair-Keimberger (iamnr3) 2013-01-21 09:13:33 UTC
I've attached the log files.
BTW, i've tried the latest ebuild but it still doesn't build. Also, when i'm typing "readelf -d /usr/lib64/libsqlite3.so | grep libpthread" into the cmd, nothing shows up...

Sqlite is build with these use flags:

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] dev-db/sqlite-3.7.14.1:3  USE="extensions fts3 readline threadsafe -debug -doc -icu -secure-delete -soundex -tcl {-test} -unlock-notify" 1,790 kB
Comment 9 Arfrever Frehtes Taifersar Arahesis 2013-01-21 17:40:25 UTC
Do not globally enable -fopenmp.