loadPCL() : segmentation fault #1524

mrcharlie90 · 2016-02-05T17:53:50Z

I would like to report this problem
http://www.pcl-users.org/segmentation-fault-in-loadPCDFile-tc4040629.html#a4040816
The following code

#include <iostream>
#include <pcl/io/pcd_io.h>
#include <pcl/point_types.h>

int main (int argc, char** argv)
{
  pcl::PointCloud<pcl::PointXYZ>::Ptr cloud (new pcl::PointCloud<pcl::PointXYZ>);

  if (pcl::io::loadPCDFile<pcl::PointXYZ> ("test_pcd.pcd", *cloud) == -1) //* load the file
  {
    PCL_ERROR ("Couldn't read file test_pcd.pcd \n");
    return (-1);
  }
  std::cout << "Loaded "
      << cloud->width * cloud->height
            << " data points from test_pcd.pcd with the following fields: "
            << std::endl;
  for (size_t i = 0; i < cloud->points.size (); ++i)
    std::cout << "    " << cloud->points[i].x
              << " "    << cloud->points[i].y
              << " "    << cloud->points[i].z << std::endl;

  return (0);
}

output a segmentation fault at pcl::io::loadPCDFile<pcl::PointXYZ> ("test_pcd.pcd", *cloud)

I've installed PCL 1.7.2 through homebrew on a Mac Pro Retina (2012) with OS X El Capitan.

When debugging the program, the problem is in the function

read (file_name, blob, ... , offset) which gives me the following error:
Exception: EXC_BAD_ACCESS (code=1, address=0x0))

in the following function (in the pcd_io.h):

read (const std::string &file_name, pcl::PointCloud<PointT> &cloud, const int offset = 0)
{
        pcl::PCLPointCloud2 blob;
        int pcd_version;
        int res = read (file_name, blob, cloud.sensor_origin_, cloud.sensor_orientation_, 
                        pcd_version, offset);

        // If no error, convert the data
        if (res == 0)
          pcl::fromPCLPointCloud2 (blob, cloud);
        return (res);
}

The text was updated successfully, but these errors were encountered:

SergioRAgostinho · 2016-02-06T00:46:06Z

Does this happen with all PCD files or only with this test_pcd.pcd you load in your code?

mrcharlie90 · 2016-02-06T01:00:35Z

All pcd files.

SergioRAgostinho · 2016-02-14T21:44:04Z

Can you try purging pcl and all its dependencies in homebrew, and reinstalling everything again. This feels like an issue in your development environment, not really a PCL bug.

cydowing · 2016-02-16T17:17:32Z

Interesting... I've got the exact same issue! and same hardware configuration

mrcharlie90 · 2016-02-16T17:22:36Z

I've tried to remove all dependencies and install it again through homebrew several times, but the segmentation fault is still there.

cydowing · 2016-02-16T18:04:44Z

Just did the same... removed PCL and all dependencies via brew. Reinstall all... got same error.

Also, to be precise, if that makes any differences, I'm using a custom point format.

pcl::PointCloud::Ptr tempCloud (new pcl::PointCloud);
pcl::io::loadPCDFile (newName, *tempCloud);

SergioRAgostinho · 2016-02-16T23:34:50Z

@mrcharlie90 & @carbomap - do you guys mind trying it with the trunk or 1.8.0-rc1?

soyersoyer · 2016-02-17T02:10:37Z

Are you using the same libc++/libstdc++ in boost_filesystem and libpcl?
You can check it with otool -L

mrcharlie90 · 2016-02-17T08:46:30Z

@SergioRAgostinho I don't know, how can I check it? I think it's the trunk version, however. I've tried to look inside the brew's formulae (which I installed through brew install pcl) and it downloads the 1.7.2 version from the following link:
https://github.com/PointCloudLibrary/pcl/archive/pcl-1.7.2.tar.gz

@soyersoyer Could you please give me the right command? I've never used otool before

cydowing · 2016-02-17T09:50:42Z

yes same here… advice on using otool would be welcome.
Indeed brew installs the 1.7.2 version. I’ve downloaded the 1.8 trunk and ready to install it… will do that later today.
Antoine

On 17 Feb 2016, at 08:46, mrcharlie90 notifications@github.com wrote:

@SergioRAgostinho https://github.com/SergioRAgostinho I don't know, how can I check it? I think it's the trunk version, however. I've tried to look inside the brew's formulae (which I installed through brew install pcl) and it downloads the 1.7.2 version from the following link:
https://github.com/PointCloudLibrary/pcl/archive/pcl-1.7.2.tar.gz x-msg://6/url
@soyersoyer https://github.com/soyersoyer Could you please give me the right command? I've never used otool before

—
Reply to this email directly or view it on GitHub #1524 (comment).

Dr Antoine Cottin
Chief Technology Officer
Carbomap Ltd.
Edinburgh Centre for Carbon Innovation
High School Yards

Edinburgh EH1 1LZ

http://www.carbomap.com
http://carbomap.wordpress.com
http://github.com/carbomap
@carbomap
+44 (0)7577 444-046

SergioRAgostinho · 2016-02-17T09:57:42Z

Basically it's as @soyersoyer mentioned. Locate boost_filesystem.dylib and pcl_io.dylib (not sure if this is the actual name but I can confirm later), and then

$ otool -L <path/to/lib.dylib>

Then copy the output here

cydowing · 2016-02-17T10:02:07Z

Here is the output:

Darkwater:~ moi$ otool -L /usr/local/Cellar/boost/1.60.0_1/lib/libboost_filesystem.dylib

/usr/local/Cellar/boost/1.60.0_1/lib/libboost_filesystem.dylib:
/usr/local/opt/boost/lib/libboost_filesystem.dylib (compatibility version 0.0.0, current version 0.0.0)
@loader_path/libboost_system.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

Darkwater:~ moi$ otool -L /usr/local/Cellar/pcl/1.7.2/lib/libpcl_io.1.7.2.dylib

/usr/local/Cellar/pcl/1.7.2/lib/libpcl_io.1.7.2.dylib:
/usr/local/opt/pcl/lib/libpcl_io.1.7.dylib (compatibility version 1.7.0, current version 1.7.2)
/usr/local/lib/libboost_system-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_filesystem-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_thread-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_date_time-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_iostreams-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_chrono-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1225.1.1)
@loader_path/libpcl_common.1.7.dylib (compatibility version 1.7.0, current version 1.7.2)
@loader_path/libpcl_io_ply.1.7.dylib (compatibility version 1.7.0, current version 1.7.2)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
/usr/local/lib/libvtkDomainsChemistry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 7.2.0)
/usr/local/lib/libhdf5.10.dylib (compatibility version 11.0.0, current version 11.1.0)
/usr/local/lib/libsz.2.dylib (compatibility version 3.0.0, current version 3.0.0)
/usr/local/lib/libhdf5_hl.10.dylib (compatibility version 11.0.0, current version 11.1.0)
/usr/local/lib/libvtkFiltersFlowPaths-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersGeneric-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersHyperTree-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersParallelImaging-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersProgrammable-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersPython-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.10)
/usr/local/lib/libvtkWrappingPython27Core-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersSelection-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersSMP-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersVerdict-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkverdict-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGeovisCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libjpeg.8.dylib (compatibility version 13.0.0, current version 13.0.0)
/usr/local/lib/libpng16.16.dylib (compatibility version 35.0.0, current version 35.0.0)
/usr/local/lib/libtiff.5.dylib (compatibility version 8.0.0, current version 8.4.0)
/usr/local/lib/libvtkproj4-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQtOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQtSQL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOSQL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtksqlite-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQtWebkit-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsQt-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsInfovis-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingMath-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingMorphological-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingStatistics-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingStencil-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInfovisBoostGraphAlgorithms-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInteractionImage-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOAMR-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOEnSight-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOExodus-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOExport-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingGL2PS-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingContextOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOImport-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOInfovis-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
/usr/local/lib/libvtkIOLSDyna-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOMINC-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOMovie-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkoggtheora-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOParallel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkjsoncpp-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOParallelXML-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOPLY-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOVideo-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingFreeTypeFontConfig-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingImage-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingLIC-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingLOD-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingQt-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingVolumeOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsContext2D-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libusb-1.0.0.dylib (compatibility version 2.0.0, current version 2.0.0)
/usr/lib/libpcap.A.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkChartsCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersImaging-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInfovisLayout-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersAMR-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkgl2ps-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInfovisCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkexoIIc-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersParallel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIONetCDF-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkNetCDF_cxx-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkNetCDF-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkParallelCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOXML-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOGeometry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOXMLParser-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOLegacy-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersTexture-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQt-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.7)
/usr/local/lib/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.7)
/usr/local/lib/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.7)
/usr/local/lib/libvtkRenderingLabel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 22.0.0)
/usr/local/lib/libvtkRenderingContext2D-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInteractionWidgets-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersHybrid-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingGeneral-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingSources-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersModeling-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingHybrid-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOImage-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkDICOMParser-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkmetaio-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInteractionStyle-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingAnnotation-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingFreeType-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkftgl-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkfreetype-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0)
/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 728.4.0)
/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingColor-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingVolume-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonColor-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersExtraction-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersStatistics-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkalglib-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingFourier-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersGeometry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersSources-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersGeneral-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonExecutionModel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonComputationalGeometry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonDataModel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonMisc-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonTransforms-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonMath-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonSystem-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtksys-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)

On 17 Feb 2016, at 09:57, Sérgio Agostinho notifications@github.com wrote:

Basically it's as @soyersoyer https://github.com/soyersoyer mentioned. Locate boost_filesystem.dylib and pcl_io.dylib (not sure if this is the actual name but I can confirm later), and then

$ otool -L <path/to/lib.dylib>
Then copy the output here

—
Reply to this email directly or view it on GitHub #1524 (comment).

Dr Antoine Cottin
Chief Technology Officer
Carbomap Ltd.
Edinburgh Centre for Carbon Innovation
High School Yards

Edinburgh EH1 1LZ

http://www.carbomap.com
http://carbomap.wordpress.com
http://github.com/carbomap
@carbomap
+44 (0)7577 444-046

SergioRAgostinho · 2016-02-17T10:08:59Z

You seem to have two boost versions installed, one through homebrew and another manually. Get rid of the manual one installed in /usr/local/lib and try reinstalling again.

cydowing · 2016-02-17T10:26:39Z

ok so what I have in /usr/local/lib are aliases pointing to my brew boost installation. actually this folder only have aliases…
So should I just remove the aliases or the actual boost folder in /usr/local/Cellar/boost?
A-

On 17 Feb 2016, at 10:09, Sérgio Agostinho notifications@github.com wrote:

You seem to have two boost versions installed, one through homebrew and another manually. Get rid of the manual one installed in /usr/local/lib and try reinstalling again.

—
Reply to this email directly or view it on GitHub #1524 (comment).

Dr Antoine Cottin
Chief Technology Officer
Carbomap Ltd.
Edinburgh Centre for Carbon Innovation
High School Yards

Edinburgh EH1 1LZ

http://www.carbomap.com
http://carbomap.wordpress.com
http://github.com/carbomap
@carbomap
+44 (0)7577 444-046

soyersoyer · 2016-02-17T16:10:02Z

When did you build the libpcl? The libsystem.B.dylib version looks different than the libboost_filesystem's, which is suspicios. Did you use the same compiler?
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1225.1.1) vs
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

cydowing · 2016-02-17T16:21:00Z

same compiler… but I just see that PCL has been updated this morning via Brew
Boost install (via brew too) dates from January 26th 2016.
A-

On 17 Feb 2016, at 16:10, soyer notifications@github.com wrote:

When did you build the libpcl? The libsystem.B.dylib version looks different than the libboost_filesystem's, which is suspicios. Did you use the same compiler?
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1225.1.1) vs
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

—
Reply to this email directly or view it on GitHub #1524 (comment).

Dr Antoine Cottin
Chief Technology Officer
Carbomap Ltd.
Edinburgh Centre for Carbon Innovation
High School Yards

Edinburgh EH1 1LZ

http://www.carbomap.com
http://carbomap.wordpress.com
http://github.com/carbomap
@carbomap
+44 (0)7577 444-046

eythor · 2016-02-23T20:42:21Z

Same issue for me. Did updating PCL to 1.8 fix it?

MacBook Pro (15-inch, Mid 2010), OS X El Capitan 10.11.3

$ brew info pcl
homebrew/science/pcl: stable 1.7.2 (bottled), HEAD

$ brew info boost
boost: stable 1.60.0 (bottled), HEAD
Collection of portable C++ source libraries
http://www.boost.org
/usr/local/Cellar/boost/1.59.0 (10,928 files, 429.2M)
Poured from bottle
/usr/local/Cellar/boost/1.60.0_1 (11,139 files, 436.0M)

$ otool -L /usr/local/Cellar/pcl/1.7.2/lib/libpcl_io.1.7.2.dylib
/usr/local/Cellar/pcl/1.7.2/lib/libpcl_io.1.7.2.dylib:
/usr/local/opt/pcl/lib/libpcl_io.1.7.dylib (compatibility version 1.7.0, current version 1.7.2)
/usr/local/lib/libboost_system-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_filesystem-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_thread-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_date_time-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_iostreams-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libboost_chrono-mt.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1225.1.1)
@loader_path/libpcl_common.1.7.dylib (compatibility version 1.7.0, current version 1.7.2)
@loader_path/libpcl_io_ply.1.7.dylib (compatibility version 1.7.0, current version 1.7.2)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
/usr/local/lib/libvtkDomainsChemistry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 7.2.0)
/usr/local/lib/libhdf5.10.dylib (compatibility version 11.0.0, current version 11.1.0)
/usr/local/lib/libsz.2.dylib (compatibility version 3.0.0, current version 3.0.0)
/usr/local/lib/libhdf5_hl.10.dylib (compatibility version 11.0.0, current version 11.1.0)
/usr/local/lib/libvtkFiltersFlowPaths-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersGeneric-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersHyperTree-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersParallelImaging-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersProgrammable-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersPython-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.10)
/usr/local/lib/libvtkWrappingPython27Core-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersSelection-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersSMP-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersVerdict-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkverdict-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGeovisCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libjpeg.8.dylib (compatibility version 13.0.0, current version 13.0.0)
/usr/local/lib/libpng16.16.dylib (compatibility version 35.0.0, current version 35.0.0)
/usr/local/lib/libtiff.5.dylib (compatibility version 8.0.0, current version 8.4.0)
/usr/local/lib/libvtkproj4-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQtOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQtSQL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOSQL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtksqlite-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQtWebkit-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsQt-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsInfovis-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingMath-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingMorphological-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingStatistics-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingStencil-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInfovisBoostGraphAlgorithms-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInteractionImage-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOAMR-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOEnSight-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOExodus-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOExport-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingGL2PS-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingContextOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOImport-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOInfovis-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
/usr/local/lib/libvtkIOLSDyna-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOMINC-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOMovie-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkoggtheora-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOParallel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkjsoncpp-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOParallelXML-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOPLY-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOVideo-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingFreeTypeFontConfig-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingImage-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingLIC-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingLOD-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingQt-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingVolumeOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsContext2D-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libusb-1.0.0.dylib (compatibility version 2.0.0, current version 2.0.0)
/usr/lib/libpcap.A.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkChartsCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersImaging-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInfovisLayout-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersAMR-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkgl2ps-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInfovisCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkexoIIc-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersParallel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIONetCDF-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkNetCDF_cxx-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkNetCDF-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkParallelCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOXML-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOGeometry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOXMLParser-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOLegacy-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersTexture-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkGUISupportQt-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.7)
/usr/local/lib/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.7)
/usr/local/lib/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.7)
/usr/local/lib/libvtkRenderingLabel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingOpenGL-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 22.0.0)
/usr/local/lib/libvtkRenderingContext2D-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkViewsCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInteractionWidgets-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersHybrid-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingGeneral-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingSources-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersModeling-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingHybrid-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOImage-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkDICOMParser-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkIOCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkmetaio-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkInteractionStyle-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingAnnotation-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingFreeType-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkftgl-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkfreetype-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0)
/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 728.4.0)
/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingColor-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingVolume-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkRenderingCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonColor-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersExtraction-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersStatistics-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkalglib-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingFourier-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkImagingCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersGeometry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersSources-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersGeneral-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkFiltersCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonExecutionModel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonComputationalGeometry-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonDataModel-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonMisc-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonTransforms-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonMath-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonSystem-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtkCommonCore-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libvtksys-6.3.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)

$ otool -L /usr/local/Cellar/boost/1.60.0_1/lib/libboost_filesystem.dylib
/usr/local/Cellar/boost/1.60.0_1/lib/libboost_filesystem.dylib:
/usr/local/opt/boost/lib/libboost_filesystem.dylib (compatibility version 0.0.0, current version 0.0.0)
@loader_path/libboost_system.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

lironesamoun · 2016-03-09T09:31:10Z

I have the same issue with PCL 1.8 compiled from the source and a Mac Pro Retina (2015) with OS X El Capitan. Do you have some news about it ?

Galto2000 · 2018-02-18T22:41:33Z

I have the same issue still using PCL 1.8, also compiled from source on Ubuntu 16.04 LTS using OpenNI-Bin-Dev-Linux-x64-v1.5.8.5.

Any ideas?

Thanks

Galto

mickeyouyou · 2019-10-21T06:35:37Z

Ubuntu 18.04 pcl 1.8 same issue.

solution is remove the boost modules and reinstall it.

and recompile pcl.

stale · 2020-05-19T09:59:29Z

Marking this as stale due to 30 days of inactivity. It will be closed in 7 days if no further activity occurs.

kunaltyagi · 2020-05-24T23:40:31Z

Issue seems to regarding broken ABI of boost libraries. Closing since it is not actionable by PCL

VictorLamoine added the kind: bug Type of issue label Feb 16, 2016

VictorLamoine mentioned this issue Feb 29, 2016

Build error on OSX #1556

Closed

SergioRAgostinho added the platform: macos label Dec 8, 2017

stale bot added the status: stale label May 19, 2020

kunaltyagi closed this as completed May 24, 2020

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loadPCL() : segmentation fault #1524

loadPCL() : segmentation fault #1524

mrcharlie90 commented Feb 5, 2016

SergioRAgostinho commented Feb 6, 2016

mrcharlie90 commented Feb 6, 2016

SergioRAgostinho commented Feb 14, 2016

cydowing commented Feb 16, 2016

mrcharlie90 commented Feb 16, 2016

cydowing commented Feb 16, 2016

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soyersoyer commented Feb 17, 2016

mrcharlie90 commented Feb 17, 2016

cydowing commented Feb 17, 2016

SergioRAgostinho commented Feb 17, 2016

cydowing commented Feb 17, 2016

SergioRAgostinho commented Feb 17, 2016

cydowing commented Feb 17, 2016

soyersoyer commented Feb 17, 2016

cydowing commented Feb 17, 2016

eythor commented Feb 23, 2016

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Galto2000 commented Feb 18, 2018

mickeyouyou commented Oct 21, 2019 •

edited

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kunaltyagi commented May 24, 2020

loadPCL() : segmentation fault #1524

loadPCL() : segmentation fault #1524

Comments

mrcharlie90 commented Feb 5, 2016

SergioRAgostinho commented Feb 6, 2016

mrcharlie90 commented Feb 6, 2016

SergioRAgostinho commented Feb 14, 2016

cydowing commented Feb 16, 2016

mrcharlie90 commented Feb 16, 2016

cydowing commented Feb 16, 2016

SergioRAgostinho commented Feb 16, 2016

soyersoyer commented Feb 17, 2016

mrcharlie90 commented Feb 17, 2016

cydowing commented Feb 17, 2016

Edinburgh EH1 1LZ

SergioRAgostinho commented Feb 17, 2016

cydowing commented Feb 17, 2016

Edinburgh EH1 1LZ

SergioRAgostinho commented Feb 17, 2016

cydowing commented Feb 17, 2016

Edinburgh EH1 1LZ

soyersoyer commented Feb 17, 2016

cydowing commented Feb 17, 2016

Edinburgh EH1 1LZ

eythor commented Feb 23, 2016

lironesamoun commented Mar 9, 2016

Galto2000 commented Feb 18, 2018

mickeyouyou commented Oct 21, 2019 • edited Loading

stale bot commented May 19, 2020

kunaltyagi commented May 24, 2020

mickeyouyou commented Oct 21, 2019 •

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