Undefined reference to LZ4_decompress_fast, LZ4_compressHC

[translunar]

I'm building on a Linux machine and getting the following errors:

[ 80%] Built target pcl_add_gaussian_noise
Linking CXX executable ../bin/pcl_boundary_estimation
../lib/libpcl_kdtree.so.1.7.2: undefined reference to `LZ4_decompress_fast'
../lib/libpcl_kdtree.so.1.7.2: undefined reference to `LZ4_compressHC'
collect2: ld returned 1 exit status
make[2]: *** [bin/pcl_boundary_estimation] Error 1
make[1]: *** [tools/CMakeFiles/pcl_boundary_estimation.dir/all] Error 2
make: *** [all] Error 2

I don't see anywhere in the CMakeCache.txt to set the LZ4 directory. I also don't see what in FLANN, but I assume this is a problem with PCL based on where the error is showing up.

[translunar]

I have not found a fix, but a workaround is to add the path to liblz4.so manually to the kdtree/CMakeFiles/pcl_kdtree.dir/link.txt file after generating my cmake build directory. This has to be repeated anytime you re-generate your cmake configuration.

[taketwo]

I wonder what is so special about your setup that you get this error. Never had it.

[VictorLamoine]

I never encountered this bug; I have no idea what can be the cause, sorry!

[translunar]

@taketwo It's a really old RedHat machine, I think.

[jspricke]

git grep -i lz4 shows only unrelated output, so I guess it's an Red Head issue. Try a newer version, maybe.

[jb4652]

At first, I met the same problem as you. But after I link flann_s.lib or flann_cpp_s.lib to PCL, no error any more. However, flann.lib and flann_cuda_s.lib still don't work.

Could anybody give an explanation?

[jspricke]

Flann includes lz4 in it's current git, but not in an official release. Which version did you use @jb4652 @mohawkjohn?

[translunar]

I was using whatever version was HEAD on git when I posted this issue.

[jb4652]

Me too, I use the most up to date master repository code, not the individual package.

[sleepyspider1]

I have this problem on windows VS2013 when building pcl_kdtree project. I needed to use the shared lib version of flann, I could not use static.

I rolled back to 1.7.1 of flann and it seemed to work. Using version 1.8.1 does not work. I had to fix a couple of things though.

1) When building debug version of flann and flann_cpp, I had to add \bigobj to the linker flags. 2) I had to add a dummy export function to the flann_cpp.cpp file so vs2013 will force output of the flann_cpp.lib import lib. If there aren't any exports, it won't create an import lib.

[kheaactua]

I still get this error with PCL>1.8.1 and FLANN 1.9.1 (four years later.) I've found that including the flann_s fixes this issue. The reason I fell upon that is that the lz4 symbols seem to only be included in that library when looking through the build scripts

I was wondering if anyone had a good solution to this? For me, I'm considering one of the following:

1. Adding flann_s to PCL's FindFLANN.cmake FLANN_LIBRARIES variable
2. Added flann_s to FLANN's exported pkg-config file (which would then inject it into FLANN_LIBRARIES)

[jspricke]

@kheaactua flann should not provide the LZ4 symbols, to begin with (see #2563 and links in there). Can you some more data? What do you compile? Which OS? Which version of PCL exactly? Which build system..

[kheaactua]

Hi @jspricke, I get this issue whenever I try to upgrade from flann 1.8.4 to flann 1.9.1. Even with PCL 1.7.2 I had to include the flann_s lib in my downstream project in order to get everything linking (though this didn't work for PCL 1.9.1)

I'm attempting to build PCL 1.9.1 (72f41b6, temporarily with a patch described in https://github.com/PointCloudLibrary/pcl/pull/2735) on Windows with MSVC 2013 using CMake, with:

• Boost 1.60
• Eigen 3.2.9
• FLANN 1.9.1
• QHULL 2015.2
• VTK 6.1
• Qt 5.3.2
• GTest 1.8.1

Also, looking at my build script, I set:

• CMAKE_CXX_STANDARD=True
• BUILD_surface_on_nurbs:BOOL=True
• PCL_BUILD_WITH_BOOST_DYNAMIC_LINKING_WIN32:BOOL=On
• BUILD_SHARED_LIBS:BOOL=True

I run this all in a Conan build script. FLANN is discovered with pkg-config (CMake output)

-- Checking for module 'flann>=1.7.0'
--   Found flann, version 1.9.1
-- FLANN found (include: C:/.conan/pdtd6xb8/1/include, lib: C:/.conan/31h03hz4/1/lib/flann_cpp_s.lib;C:/.conan/31h03hz4/1/lib/flann_s.lib)

(the flann_s.lib is there due to my attempt to get the lz4 symbols, with out a temporary patch that wouldn't be there. Also, this used to start with flann.lib, I'll comment out this patch, re-run, and get the true output)

My FLANN pkg-config file:

prefix=C:/Users/jenkins/.conan/data/flann/1.9.1/ntc/stable/package/3cf689755b8c112c8280af554277602991f652d9
exec_prefix=${prefix}
libdir=${prefix}/lib
includedir=${prefix}/include

Name: flann
Description: Fast Library for Approximate Nearest Neighbors
Version: 1.9.1
Requires:
Libs: -L${libdir} -lflann -lflann_cpp
Cflags: -I${includedir}

The specific errors are:

   "C:\.conan\wjtk1xca\1\ALL_BUILD.vcxproj" (default target) (1) ->
   "C:\.conan\wjtk1xca\1\tools\pcl_compute_cloud_error.vcxproj" (default target) (4) ->
   "C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj" (default target) (10) ->
   (Link target) ->
      kdtree_flann.obj : error LNK2001: unresolved external symbol LZ4_decompress_safe_continue [C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj]
      kdtree_flann.obj : error LNK2001: unresolved external symbol LZ4_decompress_safe [C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj]
      kdtree_flann.obj : error LNK2001: unresolved external symbol LZ4_resetStreamHC [C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj]
      kdtree_flann.obj : error LNK2001: unresolved external symbol LZ4_compress_HC_continue [C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj]
      kdtree_flann.obj : error LNK2001: unresolved external symbol LZ4_setStreamDecode [C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj]
      C:\.conan\wjtk1xca\1\bin\pcl_kdtree_release.dll : fatal error LNK1120: 5 unresolved externals [C:\.conan\wjtk1xca\1\kdtree\pcl_kdtree.vcxproj]

(more detail)

CMake Definitions:
 - CONAN_LINK_RUNTIME=/MD
 - CONAN_EXPORTED=1
 - CONAN_IN_LOCAL_CACHE=ON
 - CONAN_COMPILER=Visual Studio
 - CONAN_COMPILER_VERSION=12
 - BUILD_SHARED_LIBS=ON
 - CMAKE_INSTALL_PREFIX=C:\.conan\8qa8x8pu\1
 - CMAKE_INSTALL_BINDIR=bin
 - CMAKE_INSTALL_SBINDIR=bin
 - CMAKE_INSTALL_LIBEXECDIR=bin
 - CMAKE_INSTALL_LIBDIR=lib
 - CMAKE_INSTALL_INCLUDEDIR=include
 - CMAKE_INSTALL_OLDINCLUDEDIR=include
 - CMAKE_INSTALL_DATAROOTDIR=share
 - CONAN_CXX_FLAGS=/MP4
 - CONAN_C_FLAGS=/MP4
 - CMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
 - BOOST_ROOT:PATH=C:/.conan/vd915kie/1
 - CMAKE_CXX_STANDARD=11
 - QHULL_ROOT:PATH=C:/.conan/xyw33ogj/1
 - GTEST_ROOT:PATH=C:/.conan/lxanndul/1
 - VTK_DIR:PATH=C:/.conan/paduzfj8/1/lib/cmake/vtk-6.1
 - WITH_OPENNI:BOOL=False
 - WITH_OPENNI2:BOOL=False
 - BUILD_surface_on_nurbs:BOOL=ON
 - BUILD_SHARED_LIBS:BOOL=ON
 - PCL_BUILD_WITH_BOOST_DYNAMIC_LINKING_WIN32:BOOL=ON
 - Qt5Core_DIR:PATH=C:/.conan/be94tom9/1/lib/cmake/Qt5Core
 - Qt5Gui_DIR:PATH=C:/.conan/be94tom9/1/lib/cmake/Qt5Gui
 - Qt5OpenGL_DIR:PATH=C:/.conan/be94tom9/1/lib/cmake/Qt5OpenGL
 - Qt5Widgets_DIR:PATH=C:/.conan/be94tom9/1/lib/cmake/Qt5Widgets
 - Qt5_DIR:PATH=C:/.conan/be94tom9/1/lib/cmake/Qt5
 - QT_QMAKE_EXECUTABLE:PATH=C:/.conan/be94tom9/1/bin/qmake
 - EIGEN_INCLUDE_DIR:PATH=C:/.conan/3b7kqput/1/include/eigen3

[jspricke]

The proper solution is to add lz4 as a dependency of flann. I send a patch here: https://github.com/mariusmuja/flann/pull/399

[kheaactua]

oh, okay. I'll give that a try as soon as I can. I originally tried to deal with it by adding lz4 as a dependency in my downstream projects (making sure the dll was in my PATH on Windows), I never even thought of making it a dependency of flann.

[kheaactua]

@jspricke That patch looks great, but, it's a patch to HEAD. The last release was in 2016, are you familiar with the release cycle of FLANN at all? i.e. do you think there will be a formal release with this soon?

[jspricke]

Marius merged the patch already, but there there is not much else going on in the repo. For Debian/Ubuntu I included the patch into the package. But we can ask for a formal release if you need one.

[kheaactua]

My preference would be a formal release if that's possible - it's then easier to track as a dependency. Right now I'm just testing my builds against master. It'd probably help others too who run up against lz4 issues.

Thanks a lot

[kheaactua]

One more question about lz4 @jspricke, I don't see LZ4_INCLUDE_DIRS inserted anywhere in flann/src/cpp/CMakeLists.txt. Currently my flann build finds lz4 with pkg-config, but fails to find any of it's includes (they're not installed into system paths)

I'm going to try adding a target_include_directories(... ${LZ4_INCLUDE_DIRS}) for targets flann_cpp and flann_cpp_s, or do you think there's a better way to accomplish this?

This will be my PR: https://github.com/kheaactua/flann/commit/272937a610da194f5e346ed24c29ba42d3fb0b8b (I have it building, I just haven't tried building against flann in PCL yet)

Thanks

[jspricke]

@kheaactua you are probably right about the include dirs, On Debian lz4 is installed into the default path, so there is no need to set it explicitly. I added some comments to your patch, please ping me if you send it as a PR so I can give some more comments.

[kheaactua]

Hi @jspricke, I incorporated your comments and submited https://github.com/mariusmuja/flann/pull/400

I wanted to setup an LZ4 target, but that gave me issues with exporting.

Actually since this project is open to pull requests, there's another patch I've always been applying to flann to make it compatible with CMake 3.11+. I'll try to submit that one too.

[kevswims]

@kheaactua is there any progress on merging that pull request? I am seeing the undefined reference error to the LZ4_* stuff with a yocto recipe that I am working on for pcl.

[kheaactua]

Hi @kevswims , unfortunately no :( I was working on this as part of my last job, but I ended up changing jobs in early Feb and haven't had a chance to return to this. Worse, without that job I no longer have access to windows computers to test any changes on, etc. I hate to do this but I think I just have to abandon this PR.

[kevswims]

Hi @kheaactua thanks for the response, I tried building your fork of flann for the package I am working on and it did not seem to resolve the issue. I only need to get this working on Linux at the moment.

Is there any sort of change that can be easily made in the pcl source to get it to link properly to the LZ4 stuff as a workaround?

[kheaactua]

The only thing I remember well was PCL not making finding FLANN (especially on Windows) easy. :(

I'm not sure I got it working. All my settings were done in Conan files at conan-flann, conan-pcl, conan-build-helpers, but I unfortunately really don't remember the state I left these in. :( I do know that before I left my last job, I wasn't able to comfortably upgrade their PCL away from 1.7.2.

[taketwo]

PCL supports both old (released) and dev version of FLANN now. We have no control over the issues in FLANN itself (e.g. mariusmuja/flann#400), so closing this.

[gravit22]

I tried to compile master brunch and here is what I have:

[ 51%] Linking CXX executable ../bin/pcl_openni_planar_segmentation
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_setStreamDecode'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_compress_HC_continue'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_decompress_safe'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_decompress_safe_continue'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_resetStreamHC'
collect2: error: ld returned 1 exit status
make[2]: *** [apps/CMakeFiles/pcl_openni_planar_segmentation.dir/build.make:177: bin/pcl_openni_planar_segmentation] Error 1
make[1]: *** [CMakeFiles/Makefile2:1813: apps/CMakeFiles/pcl_openni_planar_segmentation.dir/all] Error 2
make: *** [Makefile:152: all] Error 2

What is the easiest way to deal with that?

[taketwo]

Which FLANN version do you have?

[gravit22]

1.9.1+dfsg-7. The latest one I believe.

[taketwo]

Not sure what to suggest really. Do you see lz4 in the output of ldd ../lib/libpcl_segmentation.so? If not, do you see -llz4 when running make pcl_segmentation VERBOSE=1?

[gravit22]

I have that file in the lib folder This is what I get when I try to run ldd lib/libpcl_segmentation.so

gravit@gravit-system:~/Documents/pcl/release$ ldd lib/libpcl_segmentation.so
    linux-vdso.so.1 (0x00007ffd92b35000)
    libpcl_ml.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_ml.so.1.9 (0x00007f24ac9ba000)
    libpcl_features.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_features.so.1.9 (0x00007f24a8522000)
    libpcl_filters.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_filters.so.1.9 (0x00007f24a713a000)
    libpcl_search.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_search.so.1.9 (0x00007f24a6b6a000)
    libpcl_sample_consensus.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_sample_consensus.so.1.9 (0x00007f24a5322000)
    libpcl_common.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_common.so.1.9 (0x00007f24a4f7a000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f24a4e02000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f24a4c1a000)
    libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f24a4bda000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f24a4bba000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f24a49ca000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f24a49a2000)
    libpcl_kdtree.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_kdtree.so.1.9 (0x00007f24a46da000)
    libpcl_octree.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_octree.so.1.9 (0x00007f24a426a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f24ae432000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f24a4262000)

And here what I see when I run the second command:

gravit@gravit-system:~/Documents/pcl/release$ make pcl_segmentation VERBOSE=1
/usr/bin/cmake -S/home/gravit/Documents/pcl -B/home/gravit/Documents/pcl/release --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 pcl_segmentation
make[1]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
/usr/bin/cmake -S/home/gravit/Documents/pcl -B/home/gravit/Documents/pcl/release --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /home/gravit/Documents/pcl/release/CMakeFiles 23
make -f CMakeFiles/Makefile2 segmentation/CMakeFiles/pcl_segmentation.dir/all
make[2]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make -f common/CMakeFiles/pcl_common.dir/build.make common/CMakeFiles/pcl_common.dir/depend
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cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/common /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/common /home/gravit/Documents/pcl/release/common/CMakeFiles/pcl_common.dir/DependInfo.cmake --color=
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make -f ml/CMakeFiles/pcl_ml.dir/build.make ml/CMakeFiles/pcl_ml.dir/depend
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cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/ml /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/ml /home/gravit/Documents/pcl/release/ml/CMakeFiles/pcl_ml.dir/DependInfo.cmake --color=
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make -f kdtree/CMakeFiles/pcl_kdtree.dir/build.make kdtree/CMakeFiles/pcl_kdtree.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/kdtree /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/kdtree /home/gravit/Documents/pcl/release/kdtree/CMakeFiles/pcl_kdtree.dir/DependInfo.cmake --color=
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make[3]: Nothing to be done for 'kdtree/CMakeFiles/pcl_kdtree.dir/build'.
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[ 17%] Built target pcl_kdtree
make -f octree/CMakeFiles/pcl_octree.dir/build.make octree/CMakeFiles/pcl_octree.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/octree /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/octree /home/gravit/Documents/pcl/release/octree/CMakeFiles/pcl_octree.dir/DependInfo.cmake --color=
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[ 21%] Built target pcl_octree
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cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/search /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/search /home/gravit/Documents/pcl/release/search/CMakeFiles/pcl_search.dir/DependInfo.cmake --color=
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[ 21%] Built target pcl_search
make -f sample_consensus/CMakeFiles/pcl_sample_consensus.dir/build.make sample_consensus/CMakeFiles/pcl_sample_consensus.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/sample_consensus /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/sample_consensus /home/gravit/Documents/pcl/release/sample_consensus/CMakeFiles/pcl_sample_consensus.dir/DependInfo.cmake --color=
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[ 34%] Built target pcl_sample_consensus
make -f filters/CMakeFiles/pcl_filters.dir/build.make filters/CMakeFiles/pcl_filters.dir/depend
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cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/filters /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/filters /home/gravit/Documents/pcl/release/filters/CMakeFiles/pcl_filters.dir/DependInfo.cmake --color=
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make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
make -f features/CMakeFiles/pcl_features.dir/build.make features/CMakeFiles/pcl_features.dir/build
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make[3]: Nothing to be done for 'features/CMakeFiles/pcl_features.dir/build'.
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
[ 82%] Built target pcl_features
make -f segmentation/CMakeFiles/pcl_segmentation.dir/build.make segmentation/CMakeFiles/pcl_segmentation.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/segmentation /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/segmentation /home/gravit/Documents/pcl/release/segmentation/CMakeFiles/pcl_segmentation.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
make -f segmentation/CMakeFiles/pcl_segmentation.dir/build.make segmentation/CMakeFiles/pcl_segmentation.dir/build
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make[3]: Nothing to be done for 'segmentation/CMakeFiles/pcl_segmentation.dir/build'.
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
[100%] Built target pcl_segmentation
make[2]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
/usr/bin/cmake -E cmake_progress_start /home/gravit/Documents/pcl/release/CMakeFiles 0
make[1]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'

I can't find lz4 or -llz4

[taketwo]

Thanks. Please also:

1. Post ldd lib/libpcl_search.so
2. Do rm lib/libpcl_search.so* and then make pcl_search VERBOSE=1

[gravit22]

Sure, here it is:

gravit@gravit-system:~/Documents/pcl/release$ ldd lib/libpcl_search.so
    linux-vdso.so.1 (0x00007fff050ed000)
    libpcl_octree.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_octree.so.1.9 (0x00007fad61492000)
    libpcl_kdtree.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_kdtree.so.1.9 (0x00007fad611ca000)
    libpcl_common.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_common.so.1.9 (0x00007fad60e22000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fad60caa000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fad60ac2000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fad60aa2000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fad608b2000)
    libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fad60872000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fad6084a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fad61ed2000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fad60842000)

And the second one

gravit@gravit-system:~/Documents/pcl/release$ make pcl_search VERBOSE=1
/usr/bin/cmake -S/home/gravit/Documents/pcl -B/home/gravit/Documents/pcl/release --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 pcl_search
make[1]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
/usr/bin/cmake -S/home/gravit/Documents/pcl -B/home/gravit/Documents/pcl/release --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /home/gravit/Documents/pcl/release/CMakeFiles 4
make -f CMakeFiles/Makefile2 search/CMakeFiles/pcl_search.dir/all
make[2]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make -f common/CMakeFiles/pcl_common.dir/build.make common/CMakeFiles/pcl_common.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/common /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/common /home/gravit/Documents/pcl/release/common/CMakeFiles/pcl_common.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
make -f common/CMakeFiles/pcl_common.dir/build.make common/CMakeFiles/pcl_common.dir/build
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make[3]: Nothing to be done for 'common/CMakeFiles/pcl_common.dir/build'.
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
[ 75%] Built target pcl_common
make -f octree/CMakeFiles/pcl_octree.dir/build.make octree/CMakeFiles/pcl_octree.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/octree /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/octree /home/gravit/Documents/pcl/release/octree/CMakeFiles/pcl_octree.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
make -f octree/CMakeFiles/pcl_octree.dir/build.make octree/CMakeFiles/pcl_octree.dir/build
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make[3]: Nothing to be done for 'octree/CMakeFiles/pcl_octree.dir/build'.
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
[100%] Built target pcl_octree
make -f kdtree/CMakeFiles/pcl_kdtree.dir/build.make kdtree/CMakeFiles/pcl_kdtree.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/kdtree /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/kdtree /home/gravit/Documents/pcl/release/kdtree/CMakeFiles/pcl_kdtree.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
make -f kdtree/CMakeFiles/pcl_kdtree.dir/build.make kdtree/CMakeFiles/pcl_kdtree.dir/build
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
make[3]: Nothing to be done for 'kdtree/CMakeFiles/pcl_kdtree.dir/build'.
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
[100%] Built target pcl_kdtree
make -f search/CMakeFiles/pcl_search.dir/build.make search/CMakeFiles/pcl_search.dir/depend
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
cd /home/gravit/Documents/pcl/release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gravit/Documents/pcl /home/gravit/Documents/pcl/search /home/gravit/Documents/pcl/release /home/gravit/Documents/pcl/release/search /home/gravit/Documents/pcl/release/search/CMakeFiles/pcl_search.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
make -f search/CMakeFiles/pcl_search.dir/build.make search/CMakeFiles/pcl_search.dir/build
make[3]: Entering directory '/home/gravit/Documents/pcl-trunk/release'
[100%] Linking CXX shared library ../lib/libpcl_search.so
cd /home/gravit/Documents/pcl/release/search && /usr/bin/cmake -E cmake_link_script CMakeFiles/pcl_search.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -Wabi -Wall -Wextra -Wno-unknown-pragmas -fno-strict-aliasing -Wno-format-extra-args -Wno-sign-compare -Wno-invalid-offsetof -Wno-conversion -march=native -msse4.2 -mfpmath=sse -fopenmp  -Wl,--as-needed  -shared -Wl,-soname,libpcl_search.so.1.9 -o ../lib/libpcl_search.so.1.9.1.99 CMakeFiles/pcl_search.dir/src/search.cpp.o CMakeFiles/pcl_search.dir/src/kdtree.cpp.o CMakeFiles/pcl_search.dir/src/brute_force.cpp.o CMakeFiles/pcl_search.dir/src/organized.cpp.o CMakeFiles/pcl_search.dir/src/octree.cpp.o -Wl,-rpath,/home/gravit/Documents/pcl/release/lib: /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lm ../lib/libpcl_octree.so.1.9.1.99 ../lib/libpcl_kdtree.so.1.9.1.99 ../lib/libpcl_common.so.1.9.1.99 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lm /usr/lib/x86_64-linux-gnu/libflann_cpp.so 
cd /home/gravit/Documents/pcl/release/search && /usr/bin/cmake -E cmake_symlink_library ../lib/libpcl_search.so.1.9.1.99 ../lib/libpcl_search.so.1.9 ../lib/libpcl_search.so
make[3]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
[100%] Built target pcl_search
make[2]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'
/usr/bin/cmake -E cmake_progress_start /home/gravit/Documents/pcl/release/CMakeFiles 0
make[1]: Leaving directory '/home/gravit/Documents/pcl-trunk/release'

[taketwo]

Very curious. FLANN is linked with, but not in the list of used shared objects, this is wrong. Sorry, few more commands:

• ldd lib/libpcl_kdtree.so
• nm -gDC lib/libpcl_kdtree.so | grep -i lz

[gravit22]

No problem. Sure. This is what I got.

gravit@gravit-system:~/Documents/pcl/release$ ldd lib/libpcl_kdtree.so
    linux-vdso.so.1 (0x00007ffed23fd000)
    libpcl_common.so.1.9 => /home/gravit/Documents/pcl/release/lib/libpcl_common.so.1.9 (0x00007f9159322000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f9159112000)
    libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f91590d2000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f91590b2000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9158ec2000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9158d72000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9158d4a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f9159992000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9158d42000)

gravit@gravit-system:~/Documents/pcl/release$ nm -gDC lib/libpcl_kdtree.so | grep -i lz
                 U LZ4_compress_HC_continue
                 U LZ4_decompress_safe
                 U LZ4_decompress_safe_continue
                 U LZ4_resetStreamHC
                 U LZ4_setStreamDecode

[taketwo]

And nm -gDC /usr/lib/x86_64-linux-gnu/libflann_cpp.so | grep -i lz?

[gravit22]

It shows nothing

gravit@gravit-system:~/Documents/pcl/release$ nm -gDC /usr/lib/x86_64-linux-gnu/libflann_cpp.so | grep -i lz
gravit@gravit-system:~/Documents/pcl/release$ 

[taketwo]

Hm, I'm confused about the version of FLANN that you have. You mentioned it's 1.9.1+dfsg-7. According to this page it was released in October 2018, i.e. before the PR that causes all the trouble was merged upstream. With this in mind I assumed that your FLANN still has LZ4 functions bundled in it. But according to the last command output it does not. This, in turn, means that the we are indeed missing -llz at linking step. Can you post $ cat /usr/lib/x86_64-linux-gnu/pkgconfig/flann.pc?

[gravit22]

Here it is

gravit@gravit-system:~/Documents/pcl/release$ cat /usr/lib/x86_64-linux-gnu/pkgconfig/flann.pc
# This file was generated by CMake for flann
prefix=/usr
exec_prefix=${prefix}
libdir=${prefix}/lib/x86_64-linux-gnu
includedir=${prefix}/include

Name: flann
Description: Fast Library for Approximate Nearest Neighbors
Version: 1.9.1
Requires: 
Libs: -L${libdir} -llz4 -lflann -lflann_cpp
Cflags: -I${includedir}

[taketwo]

Not a proper fix, but this may solve the problem for you. Re-run cmake passing -DFLANN_USE_STATIC=ON.

$ cmake .. -DFLANN_USE_STATIC=ON
$ make

Please let me know if this makes any difference.

[gravit22]

Unfortunately, it's not fixing it.

[ 51%] Linking CXX executable ../bin/pcl_openni_planar_segmentation
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_setStreamDecode'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_compress_HC_continue'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_decompress_safe'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_decompress_safe_continue'
/usr/bin/ld: ../lib/libpcl_segmentation.so.1.9.1.99: undefined reference to `LZ4_resetStreamHC'
collect2: error: ld returned 1 exit status
make[2]: *** [apps/CMakeFiles/pcl_openni_planar_segmentation.dir/build.make:177: bin/pcl_openni_planar_segmentation] Error 1
make[1]: *** [CMakeFiles/Makefile2:1813: apps/CMakeFiles/pcl_openni_planar_segmentation.dir/all] Error 2
make: *** [Makefile:152: all] Error 2

[taketwo]

I have some ideas about possible issues in our CMake scripts, but it won't be possible to "remote-debug" this, I'd need to reproduce it on my machine. Which OS are you using? I may try to build in a corresponding docker image.

[gravit22]

I use the last version of Ubuntu 19.04

[taketwo]

Here is a patch that should fix the problem:

diff --git a/cmake/Modules/FindFLANN.cmake b/cmake/Modules/FindFLANN.cmake
index 6e5584468..b723dc470 100644
--- a/cmake/Modules/FindFLANN.cmake
+++ b/cmake/Modules/FindFLANN.cmake
@@ -140,6 +140,11 @@ if(FLANN_FOUND)
         set_target_properties(FLANN::FLANN PROPERTIES IMPORTED_LOCATION_DEBUG "${FLANN_LIBRARY_DEBUG}")
       endif()
     endif()
+    foreach(_library ${PC_FLANN_LIBRARIES})
+      if(NOT _library MATCHES "flann")
+        set_property(TARGET FLANN::FLANN APPEND PROPERTY INTERFACE_LINK_LIBRARIES "${_library}")
+      endif()
+    endforeach()
   endif()
   get_filename_component(FLANN_ROOT "${FLANN_INCLUDE_DIR}" PATH)
 endif()

I'll send a PR later.

[gravit22]

Thanks a lot for the fast response. Now everything works.

[anujgpatil]

I made the required changes in the FIND_FLANN file but I am still getting the same error. I do have liblz4 installed (checked with apt-cache search)

[ 22%] Linking CXX executable ../../bin/pcl_hdl_viewer_simple
../../lib/libpcl_kdtree.so.1.9.1: undefined reference to `LZ4_resetStreamHC'
../../lib/libpcl_kdtree.so.1.9.1: undefined reference to `LZ4_setStreamDecode'
../../lib/libpcl_kdtree.so.1.9.1: undefined reference to `LZ4_decompress_safe'
../../lib/libpcl_kdtree.so.1.9.1: undefined reference to `LZ4_decompress_safe_continue'
../../lib/libpcl_kdtree.so.1.9.1: undefined reference to `LZ4_compress_HC_continue'

[taketwo]

Let's "replay" troubleshooting that was done in this thread. Please answer as many of the questions I have posted above as possible, starting from https://github.com/PointCloudLibrary/pcl/issues/804#issuecomment-525188532.

[anujgpatil]

Before we do that, just a little bit of background...Hopefully that should save you the hassle of deeper troubleshoot...

I'm using Jetson-UBUNTU 16.04- As suggested on #3463 ,I installed FLANN 1.9 from source using git clone and make install In the PCL's CMakeLists, I have added find_package(FLANN 1.9.0 REQUIRED) to make sure CMAKE doesn't by any chance use default FLANN version.

Now while building PCL 1.9 from source, the error first appeared in KDTREE, I could solve it by:

I have not found a fix, but a workaround is to add the path to liblz4.so manually to the kdtree/CMakeFiles/pcl_kdtree.dir/link.txt file after generating my cmake build directory. This has to be repeated anytime you re-generate your cmake configuration.

Later,I see this error at PCL_APPS, PEOPLE among many other targets. Partuclarly peculiar are these lines while building PCL:

CMake Warning (dev) at /usr/local/lib/cmake/flann/flann-targets.cmake:28 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "" will no longer be dereferenced when the policy is
  set to NEW.  Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /usr/local/lib/cmake/flann/flann-config.cmake:27 (include)
  cmake/Modules/FindFLANN.cmake:8 (find_package)
  CMakeLists.txt:288 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /usr/local/lib/cmake/flann/flann-targets.cmake:36 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "" will no longer be dereferenced when the policy is
  set to NEW.  Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /usr/local/lib/cmake/flann/flann-config.cmake:27 (include)
  cmake/Modules/FindFLANN.cmake:8 (find_package)
  CMakeLists.txt:288 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

The error is:

[ 99%] Linking CXX shared library ../lib/libpcl_segmentation.so
[ 99%] Built target pcl_segmentation
[100%] Linking CXX executable ../bin/pcl_ground_based_rgbd_people_detector
../lib/libpcl_segmentation.so.1.9.1: undefined reference to `LZ4_decompress_safe'
../lib/libpcl_segmentation.so.1.9.1: undefined reference to `LZ4_decompress_safe_continue'
../lib/libpcl_segmentation.so.1.9.1: undefined reference to `LZ4_resetStreamHC'
../lib/libpcl_segmentation.so.1.9.1: undefined reference to `LZ4_setStreamDecode'
../lib/libpcl_segmentation.so.1.9.1: undefined reference to `LZ4_compress_HC_continue'
collect2: error: ld returned 1 exit status
people/CMakeFiles/pcl_ground_based_rgbd_people_detector.dir/build.make:296: recipe for target 'bin/pcl_ground_based_rgbd_people_detector' failed
make[2]: *** [bin/pcl_ground_based_rgbd_people_detector] Error 1

You are seeing 100% because I have manually disabled certain targets to allow others to compile successfully....

Now coming to the first question-- Which FLANN version I'm using. I did install 1.9.1 from source, but I don't know how to make sure that is the one being used by CMAKE.

PS- If I try to remove the inbuilt FLANN I get these warnings:

The following packages will be REMOVED:
  libflann-dev libflann1.8
0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded.
After this operation, 17.1 MB disk space will be freed.
Do you want to continue? [Y/n] y
dpkg: warning: files list file for package 'libpcl-io1.7:arm64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpcl-visualization1.7:arm64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpcl-tracking1.7:arm64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpcl-octree1.7:arm64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpcl1.7' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpcl-kdtree1.7:arm64' missing; assuming package has no files currently installed

[taketwo]

PS- If I try to remove the inbuilt FLANN I get these warnings:

It looks like you did not correctly uninstall PCL provided by the package manager, instead just deleted its files. Try to install again with sudo apt-get install --re-install and then remove with sudo apt-get remove.

Now while building PCL 1.9 from source,

Please obtain the latest master. We don't want to debug issues that (potentially) have been solved already.

[anujgpatil]

That did it! Thanks @taketwo ..