Comments (21)
jcfr
commented on August 24, 2024
Thanks for reporting the problem.
Are you building Slicer with the docker image ? Could you provide more details to reproduce the problem ?
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fedorov
commented on August 24, 2024
@DarekDev do you have ICU installed on the system? Did you change anything in the default config settings of Slicer?
I recall in the past people experienced issues on the systems that had ICU or iconv, don't remember exactly, preinstalled.
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dmichalskii
commented on August 24, 2024
Are you building Slicer with the docker image? Could you provide more details to reproduce the problem?
Yes and I run building script from wiki page:
#!/bin/bash
ROOT_DIR=/mnt/plextor/medical/Slicer4.10
DOCKER_IMAGE=buildenv-qt5-
centos7
mkdir -p $ROOT_DIR
cd ${ROOT_DIR}
svn co http://svn.slicer.org/Slicer4/branches/Slicer-4-10 Slicer -r 27501
docker run --rm slicer/${DOCKER_IMAGE} > ~/bin/slicer-${DOCKER_IMAGE}
chmod u+x ~/bin/slicer-${DOCKER_IMAGE}
# Configure Slicer
slicer-${DOCKER_IMAGE} cmake \
-BSlicer-build -HSlicer \
-GNinja \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DBUILD_TESTING:BOOL=OFF \
-DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF \
-DSlicer_BUILD_CLI:BOOL=OFF \
-DSlicer_USE_SimpleITK:BOOL=OFF \
-DSlicer_EXTENSION_SOURCE_DIRS:STRING=${Slicer_EXTENSION_SOURCE_DIRS} \
-DSlicer_VTK_VERSION_MAJOR:STRING=9 \
-DSlicer_REQUIRED_QT_VERSION:STRING=5
# Build Slicer
slicer-${DOCKER_IMAGE} cmake --build Slicer-build
# Package Slicer
slicer-${DOCKER_IMAGE} cmake --build Slicer-build/Slicer-build --target package
@DarekDev do you have ICU installed on the system? Did you change anything in the default config settings of Slicer?
Do I need ICU on the host system? Probably not.
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jcfr
commented on August 24, 2024
Are you building Slicer with the docker image?
and I run building script from wiki page
Could you point us to the wiki page, we need to update it.
Yes and I run building script
starting with Slicer 4.10, -DSlicer_VTK_VERSION_MAJOR:STRING=9 must be changed into -DSlicer_VTK_VERSION_MAJOR:STRING=8
For reference, here are the scripts we used to create the release package:
- https://github.com/Slicer/DashboardScripts/blob/master/metroplex-slicer_4100_release_package.sh
- https://github.com/Slicer/DashboardScripts/blob/master/metroplex-slicer_4100_release_package.cmake
Do I need ICU on the host system?
You are correct, beside of docker, git and bash, no other library or executable are required on the host.
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dmichalskii
commented on August 24, 2024
Are you building Slicer with the docker image?
and I run building script from wiki page
Could you point us to the wiki page, we need to update it.
https://github.com/Slicer/SlicerBuildEnvironment#configure-build-and-package-slicer-for-linux
And why version 8? I need 9 for SlicerJupyter:
https://github.com/Slicer/SlicerJupyter#build-instructions
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jcfr
commented on August 24, 2024
And why version 8? I need 9 for SlicerJupyter:
VTK8 is the latest version of VTK, it was recently changed changed from 8 to 9 in the development branch of VTK. See http://vtk.1045678.n5.nabble.com/Re-Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-td5748714.html and http://vtk.1045678.n5.nabble.com/Re-vtkusers-Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-td5748705.html
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dmichalskii
commented on August 24, 2024
Change to 8 but still same error.
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jcfr
commented on August 24, 2024
Make sure you remove the Slicer-build directory first.
Running the following confirmed it worked
Note that I also:
- added the
DOCKER_TAGvariable to specify the tag for the docker image user to build Slicer 4.10 - remove the option
Slicer_USE_PYTHONQT_WITH_TCL, set to OFF by default in Slicer 4.10 and above
ROOT_DIR=/tmp/test-slicer-4.10-build
DOCKER_IMAGE=buildenv-qt5-centos7
DOCKER_TAG=slicer-4.10
mkdir -p $ROOT_DIR
cd ${ROOT_DIR}
svn co http://svn.slicer.org/Slicer4/branches/Slicer-4-10 Slicer -r 27501
docker run --rm slicer/${DOCKER_IMAGE}:${DOCKER_TAG} > ~/bin/slicer-${DOCKER_IMAGE}-${DOCKER_TAG}
chmod u+x ~/bin/slicer-${DOCKER_IMAGE}-${DOCKER_TAG}
# Configure Slicer
slicer-${DOCKER_IMAGE}-${DOCKER_TAG} cmake \
-BSlicer-build -HSlicer \
-GNinja \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DBUILD_TESTING:BOOL=OFF \
-DSlicer_BUILD_CLI:BOOL=OFF \
-DSlicer_USE_SimpleITK:BOOL=OFF \
-DSlicer_EXTENSION_SOURCE_DIRS:STRING=${Slicer_EXTENSION_SOURCE_DIRS} \
-DSlicer_VTK_VERSION_MAJOR:STRING=8 \
-DSlicer_REQUIRED_QT_VERSION:STRING=5
# Build DMCTK
slicer-${DOCKER_IMAGE}-${DOCKER_TAG} cmake --build Slicer-build --target DCMTK
[...]
-- Generating done
-- Build files have been written to: /work/Slicer-build/DCMTK-build
[15/18] Performing build step for 'DCMTK'
[1229/1229] Creating library symlink lib/libdcmpmap.so.13 lib/libdcmpmap.so
[16/18] No install step for 'DCMTK'
[18/18] Completed 'DCMTK'
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dmichalskii
commented on August 24, 2024
Still nothing.
I always make a clean building process.
The best thing is that this is docker image same as you have.
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jcfr
commented on August 24, 2024
Here is a gist with two CMakeCache.txt:
- top-level CMakeCache.txt
- DCMTK-build/CMakeCache.txt
https://gist.github.com/jcfr/4031c2198bbf22dae7651aa94e2547e6
It may be worth comparing with yours.
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jcfr
commented on August 24, 2024
Also just realized the version of my docker images were not matching the latest one:
slicer/buildenv-qt5-centos7 latest 3ed35ce3b252 5 weeks ago 1.453 GB
slicer/buildenv-qt5-centos7 slicer-4.10 640068f315ef 5 weeks ago 1.453 GB
https://microbadger.com/images/slicer/buildenv-qt5-centos7
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fedorov
commented on August 24, 2024
Do I need ICU on the host system?
You are correct, beside of docker, git and bash, no other library or executable are required on the host.
I was not saying you need ICU. What I meant to say is that if you have ICU installed on the system, it may cause config/build problems for Slicer. Sorry for the confusion.
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jcfr
commented on August 24, 2024
Also just realized the version of my docker images were not matching the latest one:
Seems microbadger is off, I was using the latest version.
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dmichalskii
commented on August 24, 2024
Here is a gist with two CMakeCache.txt:
* top-level CMakeCache.txt * DCMTK-build/CMakeCache.txthttps://gist.github.com/jcfr/4031c2198bbf22dae7651aa94e2547e6
It may be worth comparing with yours.
I have difference. For example:
diff CMakeCacheMY.txt CMakeCacheYOUR.txt
272c272
< DCMTK_ENABLE_CHARSET_CONVERSION:STRING=ICU
---
> DCMTK_ENABLE_CHARSET_CONVERSION:STRING=stdlibc (iconv)
353,354c353
< //Configure DCMTK with support for ICU.
< DCMTK_WITH_ICU:BOOL=ON
---
> DCMTK_WITH_ICU:BOOL=OFF
418c417
< ICU_ICU-CONFIG_EXECUTABLE:FILEPATH=/usr/bin/icu-config
---
> ICU_ICU-CONFIG_EXECUTABLE:FILEPATH=ICU_ICU-CONFIG_EXECUTABLE-NOTFOUND
421c420
< ICU_ICUINFO_EXECUTABLE:FILEPATH=/usr/bin/icuinfo
---
> ICU_ICUINFO_EXECUTABLE:FILEPATH=ICU_ICUINFO_EXECUTABLE-NOTFOUND
427c426
< ICU_INCLUDE_DIR:PATH=/usr/include
---
> ICU_INCLUDE_DIR:PATH=ICU_INCLUDE_DIR-NOTFOUND
433c432
< ICU_MAKEFILE_INC:FILEPATH=/usr/lib64/icu/50.1.2/Makefile.inc
---
> ICU_MAKEFILE_INC:FILEPATH=ICU_MAKEFILE_INC-NOTFOUND
439c438
< ICU_PKGDATA_INC:FILEPATH=/usr/lib64/icu/50.1.2/pkgdata.inc
---
> ICU_PKGDATA_INC:FILEPATH=ICU_PKGDATA_INC-NOTFOUND
655c654
< ofstd_LIB_DEPENDS:STATIC=general;/opt/qt/5.11.2/gcc_64/lib/libicuuc.so;general;/opt/qt/5.11.2/gcc_64/lib/libicudata.so;general;nsl;general;pthread;
---
> ofstd_LIB_DEPENDS:STATIC=general;nsl;general;pthread;
857c856
< DCMTK_ENABLE_CHARSET_CONVERSION-STRINGS:INTERNAL=ICU;stdlibc (iconv);<disabled>
---
> DCMTK_ENABLE_CHARSET_CONVERSION-STRINGS:INTERNAL=stdlibc (iconv);<disabled>
916c915
< DCMTK_LIBRARY_DEPENDENCIES:INTERNAL=/opt/qt/5.11.2/gcc_64/lib/libicuuc.so;/opt/qt/5.11.2/gcc_64/lib/libicudata.so;nsl;pthread
---
> DCMTK_LIBRARY_DEPENDENCIES:INTERNAL=nsl;pthread
But why there are differences? Its same image and Slicer repository.
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jcfr
commented on August 24, 2024
Making progress.
For some reason, these executables: /usr/bin/icuinfo /usr/bin/icuinfo are in your docker images, could you run the following:
docker images slicer/buildenv-qt5-centos7:slicer-4.10
and confirm that the image id is 640068f315ef
Then, could you run the following:
docker run --rm -ti slicer/buildenv-qt5-centos7:slicer-4.10 bash -c "cd /; find . | grep icu"
I expect the output to be:
./opt/qt/5.11.2/gcc_64/lib/libicudata.so
./opt/qt/5.11.2/gcc_64/lib/libicuuc.so.56
./opt/qt/5.11.2/gcc_64/lib/libicule.so
./opt/qt/5.11.2/gcc_64/lib/libicutu.so
./opt/qt/5.11.2/gcc_64/lib/libicule.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libicuio.so
./opt/qt/5.11.2/gcc_64/lib/libicui18n.so.56
./opt/qt/5.11.2/gcc_64/lib/libicule.so.56
./opt/qt/5.11.2/gcc_64/lib/libicudata.so.56
./opt/qt/5.11.2/gcc_64/lib/libicui18n.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libiculx.so
./opt/qt/5.11.2/gcc_64/lib/libicutu.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libiculx.so.56
./opt/qt/5.11.2/gcc_64/lib/libicuuc.so
./opt/qt/5.11.2/gcc_64/lib/libicui18n.so
./opt/qt/5.11.2/gcc_64/lib/libicudata.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libicutu.so.56
./opt/qt/5.11.2/gcc_64/lib/libicuio.so.56
./opt/qt/5.11.2/gcc_64/lib/libicutest.so
./opt/qt/5.11.2/gcc_64/lib/libicutest.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libicutest.so.56
./opt/qt/5.11.2/gcc_64/lib/libicuuc.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libicuio.so.56.1
./opt/qt/5.11.2/gcc_64/lib/libiculx.so.56.1
./opt/qt/5.11.2/gcc_64/include/QtFontDatabaseSupport/5.11.2/QtFontDatabaseSupport/private/qgenericunixfontdatabase_p.h
./opt/qt/5.11.2/gcc_64/include/QtThemeSupport/5.11.2/QtThemeSupport/private/qgenericunixthemes_p.h
./opt/qt/5.11.2/gcc_64/include/QtEventDispatcherSupport/5.11.2/QtEventDispatcherSupport/private/qgenericunixeventdispatcher_p.h
./opt/qt/5.11.2/gcc_64/include/QtCore/5.11.2/QtCore/private/qicucodec_p.h
./opt/qt/5.11.2/gcc_64/include/QtServiceSupport/5.11.2/QtServiceSupport/private/qgenericunixservices_p.h
./opt/qt/5.11.2/gcc_64/resources/icudtl.dat
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dmichalskii
commented on August 24, 2024
The answer is yes and yes but when I try this:
slicer-${DOCKER_IMAGE}-${DOCKER_TAG} cmake --build DCMTK
I got this:
Error: /work/DCMTK is not a directory
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jcfr
commented on August 24, 2024
I just edited my previous comment, command should be:
slicer-${DOCKER_IMAGE}-${DOCKER_TAG} cmake --build Slicer-build --target DCMTK
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dmichalskii
commented on August 24, 2024
[15/18] Performing build step for 'DCMTK'
[1229/1229] Creating library symlink lib/libdcmpmap.so.13 lib/libdcmpmap.so
[16/18] No install step for 'DCMTK'
[18/18] Completed 'DCMTK'
OK. Now I need to investigate what gone wrong. And how we resolve this problem. :)
Now all targets are building.
And of course, thank you a lot. Its
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jcfr
commented on August 24, 2024
Great 🎉 Keep us posted of your findings
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dmichalskii
commented on August 24, 2024
I get before slicer-buildenv-qt5-centos7 Dockerfile with ICU, but I thought that changing Dockerfile(removing line with yum libicu) and building image from Dockerfile overwrite existing image (with the same label and tag). Probably not, because when I set slicer-buildenv-qt5-centos7:slicer4.10 build process go further.
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JamesCTilton
commented on August 24, 2024
I'm having the same problem with my build of Slicer.
I find that I have another version of libicu** in /usr/lib64 that may be conflicting with the Slicer build.
How do I avoid this conflict (setting flag? something else?)
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Related Issues (9)
- qt5-centos7: Missing pulse, libXcomposite, libXcursor, libXtst, libXrandr and libEGL HOT 1
- DCMTK can't build do to conflict with ICU HOT 9
- Issues with qt 5.15 on linux HOT 17
- Ensure DEFAULT_DOCKCROSS_IMAGE is correctly set in image script
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