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Bug 598086 - media-libs/opencv-3.1.0-r5 - compiling of programs fails with "/usr/lib64/libgdal.so.2: undefined reference to `jp2_encode_uuid'"
Summary: media-libs/opencv-3.1.0-r5 - compiling of programs fails with "/usr/lib64/lib...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Amy Liffey
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2016-10-25 17:19 UTC by Juergen Rose
Modified: 2017-02-11 12:32 UTC (History)
1 user (show)

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


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Description Juergen Rose 2016-10-25 17:19:15 UTC
If I follow the recipe of 
http://docs.opencv.org/trunk/db/df5/tutorial_linux_gcc_cmake.html 
and try to compile a simple test programm it fails with:

rose@cheetahnew:/home_cheetahnew/rose/Txt/projects/OpenCV/Examples/samples_of_mine/DisplayImage(115)$ make
Scanning dependencies of target DisplayImage
[ 50%] Building CXX object CMakeFiles/DisplayImage.dir/DisplayImage.cpp.o
[100%] Linking CXX executable DisplayImage
/usr/lib64/libgdal.so.2: undefined reference to `jp2_encode_uuid'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/DisplayImage.dir/build.make:138: DisplayImage] Error 1
make[1]: *** [CMakeFiles/Makefile2:68: CMakeFiles/DisplayImage.dir/all] Error 2
make: *** [Makefile:84: all] Error 2

The same happens with all my other test programs, which compiled like a charm until Sep 24 2016. OpenCV changed from opencv-3.1.0-r4 to opencv-3.1.0-r5 at Sep 29 2016 on my system: Also if I add explicitly  "-lopenjp2 -lgdal -ljasper"
 to the c++ in the  Makefile call nothing is changed.

g++ -v -Werror `pkg-config --cflags opencv` $< `pkg-config --libs opencv`  -lopenjp2 -lgdal -ljasper -lm -o$@




root@cheetahnew:/root(46)# emerge --info =opencv-3.1.0-r5
Portage 2.3.2 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.23-r2, 4.8.2-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.8.2-gentoo-x86_64-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.3
KiB Mem:     7863972 total,    706508 free
KiB Swap:   50331640 total,  50203876 free
Timestamp of repository gentoo: Tue, 25 Oct 2016 02:00:01 +0000
sh bash 4.4-r1
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
distcc[2285] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Oct  2 2016 20:26:57 [disabled]
app-shells/bash:          4.4-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r2::gentoo
dev-lang/python:          2.7.12-r100::sage-on-gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.22.2::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            5.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage_cheetahnew
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

x-portage
    location: /usr/local/portage
    masters: gentoo
    priority: 0

g-cpan
    location: /var/lib/cpan
    masters: gentoo
    priority: 1

g-octave
    location: /var/lib/g-octave
    masters: gentoo
    priority: 2

lordvan
    location: /var/lib/layman/lordvan
    masters: gentoo
    priority: 50

sage-on-gentoo
    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 50

science
    location: /var/lib/layman/science
    masters: gentoo
    priority: 50

sunrise
    location: /var/lib/layman/sunrise
    masters: gentoo
    priority: 50

x11
    location: /var/lib/layman/x11
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/ext-active/ /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="-march=native -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 xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile aufs automap automount barcode bash-completion berkdb blas blast bluetooth bluray boost branding btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cilk cli cmake collada consolekit contrib cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia digitalradio djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples excel exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse gcj gd gdal gdbm gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 ithreads jadetex java jbig jit john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg opencl opencv openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python q32 qemu qhull qml qt3support qt4 qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tbb tcl tcpd tex tex4ht theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video vim-syntax virt-network virtualbox visio vorbis vpx vtk wav wayland webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xetex xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zsh-completion zvbi" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="nss" 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" GRUB_PLATFORMS="emu efi-64 pc xen" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="de en fr ru" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel" 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:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

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

media-libs/opencv-3.1.0-r5::gentoo was built with the following:
USE="contrib eigen examples ffmpeg gdal gphoto2 gstreamer gtk java jpeg jpeg2k opencl openexr opengl openmp png python qt5 threads tiff v4l vaapi vtk xine -cuda -ieee1394 (-ipp) -libav -pch -qt4 -testprograms -webp" ABI_X86="64" PYTHON_TARGETS="python2_7 python3_4 -python3_5"
Comment 1 Pavel Semerad 2016-10-31 09:58:43 UTC
I had the same problem. But I found that media-libs/jasper-1.900.6 was compiled after sci-libs/gdal-2.0.2 and this jasper version doesn't have function jp2_encode_uuid with which gdal was compiled previously. So solution is to recompile sci-libs/gdal.
Comment 2 Amy Liffey gentoo-dev 2016-10-31 10:02:53 UTC
(In reply to Pavel Semerad from comment #1)
> I had the same problem. But I found that media-libs/jasper-1.900.6 was
> compiled after sci-libs/gdal-2.0.2 and this jasper version doesn't have
> function jp2_encode_uuid with which gdal was compiled previously. So
> solution is to recompile sci-libs/gdal.

Yes indeed that is the problem. Various packages has the same problem we are working on it.
Comment 3 David Seifert gentoo-dev 2016-10-31 22:22:14 UTC
Revbump + added subslot operator should fix issues.

commit 93d2396463575b05b8c10f38fe7694b5ebe017f3
Author: David Seifert <soap@gentoo.org>
Date:   Mon Oct 31 23:01:42 2016 +0100

    sci-libs/gdal: Add sub-slot operator for media-libs/jasper
    
    Gentoo-bug: 598086, 598392