SuperBuild error at OTBQtWidget build step on Ubuntu 18.04 LTS

Description

SuperBuild error at OTBQtWidget build step on Ubuntu 18.04 LTS.

[ 76%] Linking CXX executable ../../../../bin/otbApplicationLauncherQt
//usr/lib/x86_64-linux-gnu/libpng16.so.16 : référence indéfinie vers « inflateValidate@ZLIB_1.2.9 »
collect2: error: ld returned 1 exit status
Modules/Wrappers/QtWidget/src/CMakeFiles/otbApplicationLauncherQt.dir/build.make:163: recipe for target 'bin/otbApplicationLauncherQt' failed
make[5]: *** [bin/otbApplicationLauncherQt] Error 1
CMakeFiles/Makefile2:18407: recipe for target 'Modules/Wrappers/QtWidget/src/CMakeFiles/otbApplicationLauncherQt.dir/all' failed
make[4]: *** [Modules/Wrappers/QtWidget/src/CMakeFiles/otbApplicationLauncherQt.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make[3]: *** [all] Error 2
CMakeFiles/OTB.dir/build.make:129: recipe for target 'OTB/src/OTB-stamp/OTB-build' failed
make[2]: *** [OTB/src/OTB-stamp/OTB-build] Error 2
CMakeFiles/Makefile2:395: recipe for target 'CMakeFiles/OTB.dir/all' failed
make[1]: *** [CMakeFiles/OTB.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2

Steps to reproduce

SuperBuild with this config:

export CC=`which gcc`; export CXX=`which g++`; cmake -D CMAKE_INSTALL_PREFIX=~/OTB/install -D DOWNLOAD_LOCATION=~/OTB/build/Downloads/ ../otb/SuperBuild; make

Configuration information

Ubuntu 18.04 LTS

I have also seen this "inflateValidate@ZLIB" error on my clang build...

added To Do label

I've upgraded my ubuntu to 18.04. I'll try to reproduce...

I've got a different compilation. In QT5 my error is the following:

.obj/qxcbeglwindow.o:qxcbeglwindow.cpp:vtable for QXcbEglWindow : erreur : référence à « QXcbWindow::handleXIMouseEvent(xcb_ge_event_t*, Qt::MouseEventSource) » non définie
.obj/qxcbeglwindow.o:qxcbeglwindow.cpp:vtable for QXcbEglWindow : erreur : référence à « QXcbWindow::handleXIEnterLeave(xcb_ge_event_t*) » non définie
collect2: error: ld returned 1 exit status
make[10]: *** [../../../../../../plugins/xcbglintegrations/libqxcb-egl-integration.so] Error 1

Googling the error message I did not found more info so I've tried to upgrade to Qt last stable release (5.11.1) and I've got a different compilation error (still not lucky):

.obj/qtextengine.o:qtextengine.cpp:fonction QTextEngine::itemize() const : erreur : référence à « QtPrivate::isRightToLeft(QStringView) » non définie
collect2: error: ld returned 1 exit status

Don't know what to do...

Regarding the first error reported, I suspect that some Qt library is dragging libpng16 whereas in SuperBuild we build libpng. Both depend on zlib. And since the libpng16 on bionic may be built using a more recent version of zlib, it reports a missing symbol which should be present in system zlib (but we use SuperBuild zlib).

In the QT5 superbuild we configure qt5 to use system png and system zlib which confirms your intuition :

https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/blob/develop/SuperBuild/CMake/External_qt5.cmake#L105

Should we use instead superbuild zlib and superbuild png here?

In fact it is already using SuperBuild version... it is a matter of point of view, in Qt5 build process:

• "system png" means use a png library supplied outside Qt5
• not "system png" means use a png library built by Qt5

The configure command begins with -L SB_INSTALL_PREFIX/lib -I SB_INSTALL_PREFIX/include

FYI, I had installed an Ubuntu 18.04 LTS in a VM. I had no problem to compile OTB with SuperBuild and the default configuration ; libpng is installed on my OS.

I am trying to reproduce the error in a docker container, but I am stuck somewhere in the build step of Qt5 (different error from the one reported here): link error against libQt5Core.so.5

/opt/otb/build/OTB-SuperBuild/QT5/build/qtbase/bin/qvkgen: error while loading shared libraries: libQt5Core.so.5: cannot open shared object file: No such file or directory

@mgrizonnet : did you check if your ubuntu bionic had the packages required by qtbase5-dev ?

@pasero: qtbase5-dev is installed on my bionic with the required packages. I'm a bit lost (we've got already 3 different compilation errors related to qt5 in this issue...:)

grizonnetm@pc-grizonnetm ~ $ aptitude show qtbase5-dev
Paquet : qtbase5-dev                                    
Version : 5.9.5+dfsg-0ubuntu1
État: installé
Automatiquement installé: non
Multiarchitecture : même
Priorité : optionnel
Section : libdevel
Responsable : Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture : amd64
Taille décompressée : 13,4 M
Dépend: libgl1-mesa-dev | libgl-dev, libgles2-mesa-dev | libgles2-dev, libglu1-mesa-dev | libglu-dev, libqt5concurrent5 (= 5.9.5+dfsg-0ubuntu1), libqt5core5a (= 5.9.5+dfsg-0ubuntu1), libqt5dbus5 (=
        5.9.5+dfsg-0ubuntu1), libqt5gui5 (= 5.9.5+dfsg-0ubuntu1), libqt5network5 (= 5.9.5+dfsg-0ubuntu1), libqt5printsupport5 (= 5.9.5+dfsg-0ubuntu1), libqt5sql5 (= 5.9.5+dfsg-0ubuntu1), libqt5test5 (=
        5.9.5+dfsg-0ubuntu1), libqt5widgets5 (= 5.9.5+dfsg-0ubuntu1), libqt5xml5 (= 5.9.5+dfsg-0ubuntu1), libxext-dev, qt5-qmake (= 5.9.5+dfsg-0ubuntu1), qtbase5-dev-tools (= 5.9.5+dfsg-0ubuntu1), qtchooser
Recommande: libqt5opengl5-dev (= 5.9.5+dfsg-0ubuntu1)
Suggère: default-libmysqlclient-dev, firebird-dev, libegl1-mesa-dev, libgl1-mesa-dev, libpq-dev, libsqlite3-dev, unixodbc-dev
Casse: qtbase5-dev:i386 (!= 5.9.5+dfsg-0ubuntu1)
Remplace: qtbase5-dev:i386 (< 5.9.5+dfsg-0ubuntu1)
Description : Fichiers de développement de base Qt 5
 Qt est un cadre applicatif C++ multiplate-forme. Sa principale caractéristique est son grand nombre de composants qui fournissent les fonctionnalités classiques d'une interface graphique. 
 
 Ce paquet contient les fichiers de développement d'en-tête utilisés pour la compilation d'applications Qt 5. 
 
 If you are interested in packaging Qt 5 stuff please take a look at http ://pkg-kde.alioth.debian.org/packagingqtbasedstuff.html
Site : http://qt-project.org/ 

Update : the compilation error I got was due to a configuration problem on my side (long story short: running a recent distrib in a docker with an old kernel version can be tricky).

Hopefully, I have a workaround, I'll resume digging.

Build successful on bionic docker (for those interested, the Dockerfile is attached).

@dyoussef can you check the output of ldd libQt5Gui.so in your install tree ?

ldd libQt5Gui.so
        linux-vdso.so.1 (0x00007ffcddf4e000)
        libQt5Core.so.5 => /home/david/OTB/build/QT5/build/qtbase/lib/./libQt5Core.so.5 (0x00007f2fc9a83000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2fc9864000)
        libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007f2fc95d8000)
        libpng.so.1 => not found
        libharfbuzz.so.0 => /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0 (0x00007f2fc933a000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f2fc911d000)
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f2fc8d8f000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2fc89f1000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2fc87d9000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2fc83e8000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f2fc81e4000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f2fca619000)
        libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007f2fc7fb3000)
        libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007f2fc7cfd000)
        libglib-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f2fc79e7000)
        libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f2fc7733000)
        libgraphite2.so.3 => /usr/lib/x86_64-linux-gnu/libgraphite2.so.3 (0x00007f2fc7506000)
        libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f2fc71cd000)
        libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f2fc6f5b000)
        libpng16.so.16 => /usr/lib/x86_64-linux-gnu/libpng16.so.16 (0x00007f2fc6d29000)
        libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f2fc6b01000)
        libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f2fc68fd000)
        libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f2fc66f7000)
        libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f2fc64e2000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f2fc62da000)

Ok, the problem is here, QtGui is linked to your system libfreetype, which drags libpng16. In my build is doesn't link to libfreetype (which is strange...)

ldd libQt5Gui.so
	linux-vdso.so.1 (0x00007fff7b3c4000)
	libQt5Core.so.5 => /opt/otb/install/OTB-SuperBuild/lib/./libQt5Core.so.5 (0x00007f72d694a000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f72d672b000)
	libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007f72d649f000)
	libpng.so.1 => /opt/otb/install/OTB-SuperBuild/lib/./libpng.so.1 (0x00007f72d6258000)
	libz.so.1 => /opt/otb/install/OTB-SuperBuild/lib/./libz.so.1 (0x00007f72d603c000)
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f72d5cae000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f72d5910000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f72d56f8000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f72d5307000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f72d5103000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f72d7534000)
	libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007f72d4ed2000)
	libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007f72d4c1c000)
	libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f72d48e4000)
	libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f72d46bc000)
	libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f72d44b8000)
	libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f72d42b2000)
	libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f72d409d000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f72d3e95000)

Do you have libfreetype6-dev installed ?

added Doing and removed To Do labels

Could you print the content of QT5/build/config.summary ?

Build type: linux-g++ (x86_64, CPU features: mmx sse sse2)
Configuration: use_gold_linker sse2 aesni sse3 ssse3 sse4_1 sse4_2 avx avx2 avx512f avx512bw avx512cd avx512dq avx512er avx512ifma avx512pf avx512vbmi avx512vl compile_examples enable_new_dtags f16c largefile precompile_header rdrnd shani shared rpath release c++11 c++14 c++1z concurrent reduce_exports reduce_relocations stl
Build options:
  Mode ................................... release
  Optimize release build for size ........ no
  Building shared libraries .............. yes
  Using C++ standard ..................... C++1z
  Using ccache ........................... no
  Using gold linker ...................... yes
  Using new DTAGS ........................ yes
  Using precompiled headers .............. yes
  Using LTCG ............................. no
  Target compiler supports:
    SSE .................................. SSE2 SSE3 SSSE3 SSE4.1 SSE4.2
    AVX .................................. AVX AVX2
    AVX512 ............................... F ER CD PF DQ BW VL IFMA VBMI
    Other x86 ............................ AES F16C RDRAND SHA
  Build parts ............................ tools libs
Qt modules and options:
  Qt Concurrent .......................... yes
  Qt D-Bus ............................... no
  Qt D-Bus directly linked to libdbus .... no
  Qt Gui ................................. yes
  Qt Network ............................. yes
  Qt Sql ................................. yes
  Qt Testlib ............................. yes
  Qt Widgets ............................. yes
  Qt Xml ................................. yes
Support enabled for:
  Using pkg-config ....................... yes
  QML debugging .......................... yes
  udev ................................... no
  Using system zlib ...................... yes
Qt Core:
  DoubleConversion ....................... yes
    Using system DoubleConversion ........ no
  GLib ................................... no
  iconv .................................. yes
  ICU .................................... no
  Logging backends:
    journald ............................. no
    syslog ............................... no
    slog2 ................................ no
  Using system PCRE2 ..................... no
Qt Network:
  getifaddrs() ........................... yes
  IPv6 ifname ............................ yes
  libproxy ............................... no
  OpenSSL ................................ no
    Qt directly linked to OpenSSL ........ no
  SCTP ................................... no
  Use system proxies ..................... yes
Qt Gui:
  Accessibility .......................... yes
  FreeType ............................... yes
    Using system FreeType ................ yes
  HarfBuzz ............................... yes
    Using system HarfBuzz ................ yes
  Fontconfig ............................. no
  Image formats:
    GIF .................................. yes
    ICO .................................. yes
    JPEG ................................. yes
      Using system libjpeg ............... yes
    PNG .................................. yes
      Using system libpng ................ yes
  EGL .................................... no
  OpenVG ................................. no
  OpenGL:
    Desktop OpenGL ....................... yes
    OpenGL ES 2.0 ........................ no
    OpenGL ES 3.0 ........................ no
    OpenGL ES 3.1 ........................ no
    OpenGL ES 3.2 ........................ no
  Vulkan ................................. no
  Session Management ..................... yes
Features used by QPA backends:
  evdev .................................. yes
  libinput ............................... no
  INTEGRITY HID .......................... no
  mtdev .................................. no
  tslib .................................. no
  xkbcommon-evdev ........................ no
QPA backends:
  DirectFB ............................... no
  EGLFS .................................. no
  LinuxFB ................................ yes
  VNC .................................... yes
  Mir client ............................. no
  X11:
    Using system-provided XCB libraries .. no
    EGL on X11 ........................... no
    Xinput2 .............................. yes
    XCB XKB .............................. yes
    XLib ................................. yes
    XCB render ........................... yes
    XCB GLX .............................. yes
    XCB Xlib ............................. yes
    Using system-provided xkbcommon ...... no
    Native painting (experimental) ....... no
Qt Widgets:
  GTK+ ................................... no
  Styles ................................. Fusion Windows
Qt PrintSupport:
  CUPS ................................... no
Qt Sql:
  DB2 (IBM) .............................. no
  InterBase .............................. no
  MySql .................................. no
  OCI (Oracle) ........................... no
  ODBC ................................... no
  PostgreSQL ............................. no
  SQLite2 ................................ no
  SQLite ................................. yes
    Using system provided SQLite ......... no
  TDS (Sybase) ........................... no

Note: Also available for Linux: linux-clang linux-icc

Note: Disabling X11 Accessibility Bridge: D-Bus or AT-SPI is missing.

The annoying dependency may come from system HarfBuzz. I think the correct patch is to add -no-system-harfbuzz in the Qt5 configure script.

If you want to try it, there is simple procedure:

• go to the build folder cd QT5/build
• run make uninstall
• clear the content of this directory rm -r *
• edit ../../configure_qt5.sh to add the -no-system-harfbuzz flag
• run the configure script: ../../configure_qt5.sh
• run make
• run make install

I will try to reproduce on my side.

assigned to @gpasero

Problem reproduced.

Solution: add -qt-harfbuzz in the configure script. This is only used for Linux platforms. I will prepare a MR.

cool! I'll be able to test the branch also on my ubuntu 18.04 (my error message was slightly different thant @dyoussef but it could be the same cause)

BTW I've a local branch which udpate to the last qt stable version 5.11.1 and add extra configure options to optimize the size of the output qt libs. Could perhaps be done at the same time...

sure, I can push the bug fix on your branch.

mentioned in merge request !234 (merged)

see this MR:

!234 (merged)

I've added your patch related to harfbuzz.

Should we bacport in 6.6?

closed

mentioned in merge request !391 (merged)

mentioned in issue #2081 (closed)