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IDProjectCategoryView StatusDate SubmittedLast Update
0002978Slicer4Core: Building (CMake, Superbuild)public2013-02-23 05:522014-03-06 04:54
Reportergregsharp Assigned Tojcfr  
PrioritynormalSeverityminorReproducibilityalways
Status closedResolutionfixed 
PlatformlinuxOSDebian testingOS Version
Product Version 
Target VersionSlicer 4.3.0Fixed in VersionSlicer 4.3.0 
Summary0002978: Build error & unstable executable on linux
Description

Debian testing, 64-bit

  • kernel version 3.2.0-4-amd64
  • gcc 4.7.2

The build emits the following error:

Linking CXX executable ../../../lib/Slicer-4.2/cli-modules/DTIimport
/home/gsharp/build/slicer-4/Slicer-build/ITKv4-build/lib/libITKIODCMTK-4.4.so.1: undefined reference to OFFilename::OFFilename(char const*, bool)' /home/gsharp/build/slicer-4/Slicer-build/ITKv4-build/lib/libITKIODCMTK-4.4.so.1: undefined reference toOFFilename::~OFFilename()'
collect2: error: ld returned 1 exit status
make[5]: *** [lib/Slicer-4.2/cli-modules/DTIexport] Error 1

If one proceeds (using make -k) and builds the slicer executable, it crashes after the first splash screen with the following error.

$ ./Slicer-build/Slicer
error: [/home/gsharp/build/slicer-4/Slicer-build/Slicer-build/bin/./SlicerApp-real] exit abnormally - Report the problem.

Additional Information

I found the problem. ITK build is using the wrong dcmtk. Here is what's in the ITK CMakeCache:

DCMTK_dcmdata_LIBRARY:FILEPATH=/usr/lib/libdcmdata.so

It should be something like this:

DCMTK_dcmdata_LIBRARY:FILEPATH=/home/gsharp/build/slicer-4/Slicer-build/DCMTK-install/lib/libdcmdata.a

TagsITKv4

Relationships

related to 0002883 closedjcfr Fix FindDCMTK.cmake provided by ITKv4 

Activities

hjmjohnson

hjmjohnson

2013-02-23 11:43

developer   ~0008014

DTIImport is a tool that JC and Sonia wrote at a Summer programmer week a few years ago. I don't think it is still needed.

If linkage is wrong, then I think that somethign is not being passed correctly. DCMTK is undergoing other fixes right now that may make this problem easier to fix, and JC is informed on that as well.
jcfr

jcfr

2013-02-23 11:58

administrator   ~0008017

Last edited: 2013-02-23 11:59

@hans: Don't recall writing such a tool :p And as you said, the underlying is within ITKv4 and the way it handles DCMTK. That is why the issue was assigned to you :)

See https://github.com/Slicer/Slicer/blob/master/Modules/CLI/DTIImportExport/CMakeLists.txt
jcfr

jcfr

2013-02-23 12:02

administrator   ~0008018

Waiting for ITKv4 folks to fix issue 0002883.
hjmjohnson

hjmjohnson

2013-02-23 12:03

developer   ~0008019

JC,

Perhaps updating ITK will fix this. We ran into what looks like a similar issue lately, Brad King helped us track down and fix some of the USE_SYSTEM_DCMTK magic for linking properly. That work led to the realization that fixing DCMTK itself was the most effective course of action.

Hans
jcfr

jcfr

2013-02-23 12:07

administrator   ~0008020

Few days ago, ITKv4 checked out by has already been updated to the latest commit of the release branch. See https://github.com/Slicer/Slicer/commit/b2eed860968c7d06714e2dff8a1cfa1935bf77fc

Do not hesitate to provide me with a patch.
jcfr

jcfr

2013-02-23 19:22

administrator   ~0008022

Fixed in r21772
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21772
jcfr

jcfr

2014-03-06 04:53

administrator   ~0010777

Closing resolved issues that have not been updated in more than 3 months

Issue History

Date Modified Username Field Change
2013-02-23 05:52 gregsharp New Issue
2013-02-23 05:52 gregsharp Status new => assigned
2013-02-23 05:52 gregsharp Assigned To => jcfr
2013-02-23 11:39 jcfr Assigned To jcfr => hjmjohnson
2013-02-23 11:39 jcfr Target Version => Slicer 4.3.0
2013-02-23 11:39 jcfr Tag Attached: ITKv4
2013-02-23 11:42 hjmjohnson Assigned To hjmjohnson => jcfr
2013-02-23 11:43 hjmjohnson Note Added: 0008014
2013-02-23 11:54 jcfr Relationship added related to 0002883
2013-02-23 11:58 jcfr Note Added: 0008017
2013-02-23 11:59 jcfr Note Edited: 0008017
2013-02-23 12:02 jcfr Note Added: 0008018
2013-02-23 12:02 jcfr Status assigned => feedback
2013-02-23 12:03 hjmjohnson Note Added: 0008019
2013-02-23 12:07 jcfr Note Added: 0008020
2013-02-23 19:22 jcfr Note Added: 0008022
2013-02-23 19:22 jcfr Status feedback => resolved
2013-02-23 19:22 jcfr Fixed in Version => Slicer 4.3.0
2013-02-23 19:22 jcfr Resolution open => fixed
2014-03-06 04:53 jcfr Note Added: 0010777
2014-03-06 04:54 jcfr Status resolved => closed