Arch Linux User Repository

@bartus Yes, I think you're right. dcmtk needs to be compiled with gcc12 too. dcmtk is build with gcc 12 when I build 3dslicer at that time (gcc 13 is not in official repo yet), so I did not encounter this issue. You could rebuild dcmtk with gcc12, and this issue would be fixed.

Got missing symbol error while linking dcmtk:libofstd.so

[ 92%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkTreeComboBoxPlugin.cpp.o
[ 92%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkSearchBoxPlugin.cpp.o
[ 93%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkSettingsPanelPlugin.cpp.o
/usr/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/12.3.0/../../../../lib/libofstd.so: undefined reference to `std::ios_base_library_init()@GLIBCXX_3.4.32'
[ 93%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkSettingsDialogPlugin.cpp.o
[ 93%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkSliderWidgetPlugin.cpp.o
[ 93%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkWorkflowButtonBoxWidgetPlugin.cpp.o
[ 93%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/moc_ctkWorkflowWidgetStepPlugin.cpp.o
[ 93%] Building CXX object Libs/Widgets/Plugins/CMakeFiles/CTKWidgetsPlugins.dir/qrc_ctkWidgetsPlugins.cpp.o
collect2: error: ld returned 1 exit status
make[8]: *** [Applications/ctkDICOM/CMakeFiles/ctkDICOM.dir/build.make:108: bin/ctkDICOM] Error 1
make[7]: *** [CMakeFiles/Makefile2:1195: Applications/ctkDICOM/CMakeFiles/ctkDICOM.dir/all] Error 2
make[7]: *** Waiting for unfinished jobs....

Should dcmtk be compiled with gcc-12 or is this a missing -lstdc++ flag in cmake?

$nm -CD /usr/lib/libstdc++.so.6|grep ios_base_library                                                                                                                                   
00000000000c2460 T std::ios_base_library_init()@@GLIBCXX_3.4.32
$pacown /usr/lib/libstdc++.so.6                                                                                                                                                         
/usr/lib/libstdc++.so.6 is owned by gcc-libs 13.1.1-2

@viper2642 Your build log is not enough for debugging.

I get the following build error:

[ 13%] Built target CommonCore-objects
[ 13%] Linking C shared library ../../../../lib/libvtkhdf5-9.1.so
[ 13%] Built target vtkhdf5_src
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/VTK.dir/build.make:91: VTK-prefix/src/VTK-stamp/VTK-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:726: CMakeFiles/VTK.dir/all] Error 2
make: *** [Makefile:91: all] Error 2
make: Leaving directory '/home/dpfeffer/.cache/yay/3dslicer/src/build'
==> ERROR: A failure occurred in build().
Aborting...
 -> error making: 3dslicer-exit status 4
 -> Failed to install the following packages. Manual intervention is 
required:
3dslicer - exit status 4

@maverick1 I found one of the cmake build scripts expects the source to be in a git repo to set Slicer_WC_LAST_CHANGED_DATE. When using the release tarball I had to git init && git add . && git commit -m "dummy" in the extracted source dir to get it to build.

Directly download the tarball from the assets rather than using git to fetch it. The link to the source coder for the version 5.2.2 is https://github.com/Slicer/Slicer/archive/refs/tags/v5.2.2.tar.gz

@hottea not sure what happen left it to build for a good 30mins + but system rebooted it might be related to system libffi. Not a software I would often use so just running the prebuilt package from official site, I just would've liked it to be installed on AUR. Might give it another go in future updates. :(

@techz Could you build it in a clean chroot as described in this wiki. The latest build works as expected. It seems 3dslicer did not work with the system libffi.

Not sure if this has been a issue in the past but I am currently getting a build error:

[ 66%] Building ASM object CMakeFiles/objlib.dir/src/x86/unix64.S.o
/home/techz/.cache/yay/3dslicer/src/build/LibFFI/src/x86/unix64.S: Assembler messages:
/home/techz/.cache/yay/3dslicer/src/build/LibFFI/src/x86/unix64.S:581: Error: junk at end of line, first unrecognized character is `@'
/home/techz/.cache/yay/3dslicer/src/build/LibFFI/src/x86/unix64.S:600: Error: junk at end of line, first unrecognized character is `@'
/home/techz/.cache/yay/3dslicer/src/build/LibFFI/src/x86/unix64.S:613: Error: junk at end of line, first unrecognized character is `@'
/home/techz/.cache/yay/3dslicer/src/build/LibFFI/src/x86/unix64.S:627: Error: junk at end of line, first unrecognized character is `@'
/home/techz/.cache/yay/3dslicer/src/build/LibFFI/src/x86/unix64.S:640: Error: junk at end of line, first unrecognized character is `@'
make[5]: *** [CMakeFiles/objlib.dir/build.make:173: CMakeFiles/objlib.dir/src/x86/unix64.S.o] Error 1
make[5]: Leaving directory '/home/techz/.cache/yay/3dslicer/src/build/LibFFI-build'
make[4]: *** [CMakeFiles/Makefile2:87: CMakeFiles/objlib.dir/all] Error 2
make[4]: Leaving directory '/home/techz/.cache/yay/3dslicer/src/build/LibFFI-build'
make[3]: *** [Makefile:136: all] Error 2
make[3]: Leaving directory '/home/techz/.cache/yay/3dslicer/src/build/LibFFI-build'
make[2]: *** [CMakeFiles/LibFFI.dir/build.make:90: LibFFI-prefix/src/LibFFI-stamp/LibFFI-build] Error 2
make[2]: Leaving directory '/home/techz/.cache/yay/3dslicer/src/build'
make[1]: *** [CMakeFiles/Makefile2:562: CMakeFiles/LibFFI.dir/all] Error 2
make[1]: Leaving directory '/home/techz/.cache/yay/3dslicer/src/build'
make: *** [Makefile:91: all] Error 2
make: Leaving directory '/home/techz/.cache/yay/3dslicer/src/build'
==> ERROR: A failure occurred in build().
    Aborting...
 -> error making: 3dslicer

@entshuld I just update the PKGBUILD, you could re-try, and it should work.