DCMTK won't build if Anaconda is installed
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	kalali
	Oct 18 2018, 2:55 PM

Description

Using the latest beta-branch the superbuild fails during linking of ofchrenc.obj in project DCMTK.
e.g.
ofchrenc.obj : error LNK2019: unresolved external symbol ucnv_convertEx_58 referenced in function "public: class OFCondition __cdecl OFCharacterEncoding::Implementation::convert

The reason for this seems to be that DCMTK_ENABLE_CHARSET_CONVERSION is defined inside bin\ep\src\DCMTK-build\config\include\dcmtk\config\osconfig.h. I suspect this has something to do with DCMTK_WITH_ICU being set to ON inside bin\ep\src\DCMTK\CMakeLists.txt.
This might happen when anaconda is installed, so it was finding the anacoda versions of binaries (ICU Conversion).

A possible solution would be to force the value to be OFF by using -DDCMTK_WITH_ICU:BOOL=OFF inside src\CMakeExternals\DCMTK.cmake

Related Objects

Mentioned In: T27033: Clean up stale remote branches
T26438: DCMTK disable ICU
Mentioned Here: T26438: DCMTK disable ICU

Event Timeline

kalali triaged this task as Normal priority.Oct 18 2018, 2:55 PM

kalali created this task.

Thanks a lot, solution works for me. Is there any reason to not add the fix to the master?

I think this bug is quite critical, because anaconda is needed for many applications. I use it for Anser EMT (open source tracker) and pytorch.

franza raised the priority of this task from Normal to Unbreak Now!.May 30 2019, 12:38 PM

franza claimed this task.May 30 2019, 12:40 PM

Pushed new branch T25535-FixLinkerErrorWhenAnacondaIsInstalled.

I can't think of any reason. I just stumbled upon this and suggested the fix. Since I have no experience with Anaconda or DCMTK I wasn't sure if this is the correct way to fix it or if there are any side effects. Maybe a review would have been a good idea. Maybe @nolden can help?

I think it is not the best idea to get rid of ICU as it has its purpose regarding Unicode handling. If building or finding ICU interferes with an installation of Anaconda, there are probably other ways of telling DCMTK through CMake to behave as expected.

kalali mentioned this in T26438: DCMTK disable ICU.Jul 2 2019, 11:55 AM

Sorry for jumping in late. I'm afraid currently we are anyway not testing any encoding stuff sufficiently.

You could test the following. Go to https://www.dclunie.com/ and look for this section:

"Internationalized character set test DICOM images and what the names should look like"

In general I would suggest we could change defaults to a more relaxed setting, but maybe for Release builds we should think about a solution how to include these libraries if it turns out they are necessary even for basic Umlaute handling

Ich sah hier was ähnliches, beim MITK bauen auf meiner ubuntu-OpenStack-Instanz, allerdings ohne Anaconda, mit gcc 7 (g++-7/gcc-7 version g++-7 (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0): undefined reference to `ucnv_convertEx*'

[ 30%] Building C object src/CMakeFiles/hdf5-shared.dir/H5AC.c.o
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_TO_U_CALLBACK_SKIP_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_FROM_U_CALLBACK_STOP_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_getName_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_close_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_convertEx_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_open_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_getFromUCallBack_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_setToUCallBack_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `u_errorName_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_FROM_U_CALLBACK_SKIP_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_setFromUCallBack_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_TO_U_CALLBACK_STOP_63'
collect2: error: ld returned 1 exit status
make[5]: *** [ofstd/tests/CMakeFiles/ofstd_tests.dir/build.make:430: bin/ofstd_tests] Fehler 1
make[4]: *** [CMakeFiles/Makefile2:307: ofstd/tests/CMakeFiles/ofstd_tests.dir/all] Fehler 2
make[3]: *** [Makefile:141: all] Fehler 2
make[2]: *** [CMakeFiles/DCMTK.dir/build.make:115: ep/src/DCMTK-stamp/DCMTK-build] Fehler 2
make[1]: *** [CMakeFiles/Makefile2:327: CMakeFiles/DCMTK.dir/all] Fehler 2
make[1]: *** Es wird auf noch nicht beendete Prozesse gewartet....
[ 30%] Building C object src/CMakeFiles/hdf5-shared.dir/H5B.c.o

[  0%] Performing build step for 'DCMTK'
[  2%] Built target ofstd
[  2%] Linking CXX executable ../../bin/ofstd_tests
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_TO_U_CALLBACK_SKIP_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_FROM_U_CALLBACK_STOP_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_getName_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_close_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_convertEx_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_open_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_getFromUCallBack_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_setToUCallBack_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `u_errorName_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_FROM_U_CALLBACK_SKIP_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `ucnv_setFromUCallBack_63'
/usr/bin/ld: ../../lib/libofstdd.so.3.6.3: undefined reference to `UCNV_TO_U_CALLBACK_STOP_63'
collect2: error: ld returned 1 exit status
make[6]: *** [ofstd/tests/CMakeFiles/ofstd_tests.dir/build.make:430: bin/ofstd_tests] Fehler 1
make[5]: *** [CMakeFiles/Makefile2:307: ofstd/tests/CMakeFiles/ofstd_tests.dir/all] Fehler 2
make[4]: *** [Makefile:141: all] Fehler 2
make[3]: *** [CMakeFiles/DCMTK.dir/build.make:115: ep/src/DCMTK-stamp/DCMTK-build] Fehler 2
make[2]: *** [CMakeFiles/Makefile2:327: CMakeFiles/DCMTK.dir/all] Fehler 2
make[1]: *** [CMakeFiles/Makefile2:339: CMakeFiles/DCMTK.dir/rule] Fehler 2
make: *** [Makefile:255: DCMTK] Fehler 2

Nach einem tieferen Blick in (...)/ep/src/DCMTK-build/ kam ich auf folgende Lösung: CMAKE_CXX_FLAGS:STRING=-Wno-error=deprecated-declarations

Update2:
Habe ep/src/DCMTK-*/ gelöscht und dann im MitkSuperBuild/ "cmake ." und "make DCMTK" aufgerufen und DCMTK hat einwandfrei korrekt gebaut, sowohl mit als auch ohne Conda auf dem build system.

Speculating:
Maybe that was a bash environment side effect, i cannot reproduce this error on my GNU/Linux system where I use tcsh instead of bash.
The tcsh environment does not contain anything "conda" related, while bash does, if (ana|mini)conda is installed.

@kislinsk @nolden : Could you please comment on the fix in T26438?

kislinsk lowered the priority of this task from Unbreak Now! to Normal.Nov 4 2019, 9:42 AM

kislinsk mentioned this in T27033: Clean up stale remote branches.Jan 25 2020, 9:00 PM

Hi there! 🙂

This task was auto-closed according to our Task Lifecycle Management.
Please follow this link for more information and don't forget that you are encouraged to reasonable re-open tasks to revive them. 🚑

Best wishes,
The MITK devs

The bug has been fixed, hasn't it? I'll set it to "resolved", if someone still has problems with it, she or he can reopen the bug.

DCMTK won't build if Anaconda is installedClosed, ResolvedPublicActions

Description

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Event Timeline

DCMTK won't build if Anaconda is installed
Closed, ResolvedPublic
Actions