Package Details: 3dslicer 5.6.2-2

Git Clone URL: https://aur.archlinux.org/3dslicer.git (read-only, click to copy)
Package Base: 3dslicer
Description: A free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research
Upstream URL: https://www.slicer.org
Licenses: BSD-3-Clause
Submitter: tmladek
Maintainer: hottea (lilac)
Last Packager: lilac
Votes: 20
Popularity: 0.058176
First Submitted: 2015-01-21 08:58 (UTC)
Last Updated: 2024-05-20 21:23 (UTC)

Latest Comments

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hottea commented on 2023-07-25 04:29 (UTC)

@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.

bartus commented on 2023-07-24 15:00 (UTC) (edited on 2023-07-24 15:02 (UTC) by bartus)

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

hottea commented on 2023-05-27 07:19 (UTC)

@viper2642 Your build log is not enough for debugging.

viper2642 commented on 2023-05-24 07:48 (UTC)

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

snth commented on 2023-04-27 21:06 (UTC)

@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.

rabin commented on 2023-02-28 16:00 (UTC)

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

techz commented on 2022-07-07 07:28 (UTC)

@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. :(

hottea commented on 2022-07-07 05:13 (UTC) (edited on 2022-07-07 05:16 (UTC) by hottea)

@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.

techz commented on 2022-07-07 02:50 (UTC) (edited on 2022-07-07 02:50 (UTC) by techz)

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

hottea commented on 2022-06-28 00:42 (UTC)

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