Bug 499448 – sci-libs/gdal-1.10.1 "USE=-threads ecwj2k" - ld: /usr/lib64/libNCSUtil.so: undefined reference to symbol 'pthread_cancel@@GLIBC_2.2.5'

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Jean-Claude Repetto 2014-01-27 13:29:58 UTC]

When the use flag "threads" is not enabled, gdal-1.10.1 fails to build with the following error message :

/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libNCSUtil.so: undefined reference to symbol 'pthread_cancel@@GLIBC_2.2.5'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/../../../../x86_64-pc-linux-gnu/bin/ld: note: 'pthread_cancel@@GLIBC_2.2.5' is defined in DSO /lib64/libpthread.so.0 so try adding it to the linker command line
/lib64/libpthread.so.0: could not read symbols: Invalid operation



$ emerge -pv gdal

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

Calculating dependencies... done!
[ebuild  N    ~] sci-libs/gdal-1.10.1  USE="aux_xml ecwj2k geos gif jpeg pdf png python spatialite sqlite -armadillo -curl -debug -doc -fits -gml -hdf5 -java -jpeg2k -mdb -mysql -netcdf -odbc -ogdi -opencl -perl -postgres -ruby -threads -xls" PYTHON_TARGETS="python2_7 python3_3 -python2_6 -python3_2" 0 kB



Reproducible: Always

Steps to Reproduce:
1. unset the USE flag "threads"
2. emerge gdal-1.10.1

[Comment 1 Jean-Claude Repetto 2014-01-27 13:30:42 UTC]

# emerge --info
Portage 2.2.7 (default/linux/amd64/13.0/desktop/kde, gcc-4.6.3, glibc-2.17, 3.10.7-gentoo-r1 x86_64)
=================================================================
System uname: Linux-3.10.7-gentoo-r1-x86_64-Intel-R-_Xeon-R-_CPU_E5-1620_0_@_3.60GHz-with-gentoo-2.2
KiB Mem:     2052348 total,    249112 free
KiB Swap:   15623208 total,  15476792 free
Timestamp of tree: Mon, 27 Jan 2014 09:00:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
app-shells/bash:          4.2_p45
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.7.5-r3, 3.2.5-r3, 3.3.3
dev-util/cmake:           2.8.11.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.12.6, 1.13.4
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.6.3, 4.7.3-r1
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo java seden rion x-portage
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
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"
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 preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="fr_FR.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-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="/var/lib/layman/java /var/lib/layman/seden /var/lib/layman/rion /usr/local/portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib cups cxx dbus declarative dri dts dvd dvdr ecwj2k emboss encode exif fam firefox flac fortran gdbm gif gpm gtk iconv jpeg kde kipi lcms libnotify mad mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds python qt3support qt4 readline sdl semantic-desktop session spatialite spell sqlite sse sse2 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="64" 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" 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 author" 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 ublox 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="fr" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="virtualbox" 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, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

[Comment 2 Jeroen Roovers (RETIRED) 2014-01-27 13:41:10 UTC]

Please attach the entire build log to this bug report.

[Comment 3 Jean-Claude Repetto 2014-01-27 14:04:24 UTC]

Created attachment 368870 [details]
Complete build log

[Comment 4 Aaron W. Swenson 2014-01-27 14:39:13 UTC]

(In reply to Jean-Claude Repetto from comment #3)
> Created attachment 368870 [details]
> Complete build log

I don't think this would resolve it, but please try rebuilding with MAKEOPTS=-j1.

[Comment 5 Jeroen Roovers (RETIRED) 2014-01-27 14:57:49 UTC]

(In reply to Aaron W. Swenson from comment #4)
> I don't think this would resolve it, but please try rebuilding with
> MAKEOPTS=-j1.

No, it wouldn't.

[Comment 6 Jean-Claude Repetto 2014-01-27 17:04:04 UTC]

Maybe the threads library should be added when the ecwj2k USE flag is set ?

[Comment 7 Aaron W. Swenson 2014-01-27 17:47:45 UTC]

(In reply to Jean-Claude Repetto from comment #6)
> Maybe the threads library should be added when the ecwj2k USE flag is set ?

I can do that.

[Comment 8 Aaron W. Swenson 2014-01-27 23:05:14 UTC]

  27 Jan 2014; Aaron W. Swenson <[e-mail]> gdal-1.10.1.ebuild:
  Fix bug 499448: REQUIRED_USE on threads with ecwj2k
  Fix bug 499454: Add a leading space to MAKEOPTS

Resync