CamiTK Community Edition issueshttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues2024-02-23T11:13:30+01:00https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/117Update upstream-ci/master in order to fix package build2024-02-23T11:13:30+01:00Emmanuel PromayonUpdate upstream-ci/master in order to fix package build## About you
CamiTK dev & maintainer
## Overview
## Steps to Reproduce
See error for instance in Job [#187192](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/187192) failed for f1e1a157f156667c4c74908c54343597739b4...## About you
CamiTK dev & maintainer
## Overview
## Steps to Reproduce
See error for instance in Job [#187192](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/187192) failed for f1e1a157f156667c4c74908c54343597739b4412:
## Actual VS Expected Result
no package build vs debian unstable package are build
## Relevant logs and/or screenshots
See error for instance in Job [#187192](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/187192) failed for f1e1a157f156667c4c74908c54343597739b4412:
## Interpretation & Possible fixes
- Check lintian message
- Check d/r
It seems the first time the package build failed was after !156 was merged, see #109
## CamiTK Version
Current development as of 23 dec 2020
## Latest info
As of 1 feb 2021
Job [#197871](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871) failed for 45108ed033f366a2c065e14aae61c1fd7c83255b:
The package was not generated, please check the artifacts and fix the problem:
- summary: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/packaging-debian-unstable-develop/log/summary.log
- check environment: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/packaging-debian-unstable-develop/log/check-environment.log
- build package: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/packaging-debian-unstable-develop/log/build-package.log
- prepare package environment: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/packaging-debian-unstable-develop/log/prepare-package-environment.log
---
**please do not remove anything below this line**CamiTK 5Emmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/133imp and actionstatemachine requires linking with specific viewers2023-11-29T11:23:11+01:00Emmanuel Promayonimp and actionstatemachine requires linking with specific viewers## About you
camitk developer
## Overview
imp and actionstatemachine requires linking with specific viewers.
This means they are _linked_ to for instance medicalimageviewer lib.
This is not admissible as this means LD_LIBRARY_PATH ha...## About you
camitk developer
## Overview
imp and actionstatemachine requires linking with specific viewers.
This means they are _linked_ to for instance medicalimageviewer lib.
This is not admissible as this means LD_LIBRARY_PATH has to be modified to include lib/camitk-x.y/viewers which is not a standard or easy thing to set.
## Steps to Reproduce
`ldd -r bin/camitk-imp` shows the dependencies
## Actual VS Expected Result
sdk applications should not have to be linked to viewers.
**Note** This might be ok for CEP applications (very rare case, see `tutorials/applications/fancy` for an example where this might be required).
## Relevant logs and/or screenshots
Test using docker:
```bash
$ docker pull gricad-registry.univ-grenoble-alpes.fr/camitk/camitk/camitk-lts:5.1
$ docker run --privileged=true --rm -v /tmp/.X11-unix:/tmp/.X11-unix -v ./build:/home/camitk/build -w /home/camitk/build -e "LD_LIBRARY_PATH=/home/camitk/build/lib" -e "DISPLAY=:0" -ti gricad-registry.univ-grenoble-alpes.fr/camitk/camitk/camitk-lts:5.1 bin/camitk-config --version
bin/camitk-config build using CamiTK 5.1.dev.develop.db3bf90b
$ docker run --privileged=true --rm -v /tmp/.X11-unix:/tmp/.X11-unix -v ./build:/home/camitk/build -w /home/camitk/build -e "LD_LIBRARY_PATH=/home/camitk/build/lib" -e "DISPLAY=:0" -ti gricad-registry.univ-grenoble-alpes.fr/camitk/camitk/camitk-lts:5.1 bin/camitk-imp --version
bin/camitk-imp: error while loading shared libraries: libactionviewer.so.5: cannot open shared object file: No such file or directory
```
## Interpretation & Possible fixes
For sdk application only user `Viewer` API and do not use specific method.
That might means a rewrite of `MedicalImageViewer::setToolbarAutoVisibility` and `MedicalImageViewer::setToolBarVisibility`
Even if this might mean few duplicated lines, check if it possible to also remove dependencies to Medical Image Viewer in `tutorials/applications/fancy` as well.
## CamiTK Version
CamiTK 5.1.dev.develop.db3bf90b
---
**please do not remove anything below this line**Emmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/145Update testing to debian stable (bookworm)2023-06-16T13:26:50+02:00Emmanuel PromayonUpdate testing to debian stable (bookworm)| | |
|--|--|
| **As a** | CamiTK developer |
| **I would like to** | Have a stable debian bookworm docker in the CI gitlab runner |
| **So that** | I can make sure that the CI works on the (new) current stable version of debian |
| **Ep...| | |
|--|--|
| **As a** | CamiTK developer |
| **I would like to** | Have a stable debian bookworm docker in the CI gitlab runner |
| **So that** | I can make sure that the CI works on the (new) current stable version of debian |
| **Epic/Topics** | [topic keywords or project epic] |
## Description / Overview
Debian 12.0 (codename bookworm) is [released](https://www.debian.org/releases/bookworm/)
CI should be using this version instead of testing (that should not make any difference, but it seems "cleaner")
## Hints
- create new docker image from debian stable
- push it to this project repository
- pull it from the CI VM
- re-install gitlab runner
## Acceptance tests
- [x] new docker image is available in the project repository
- [x] gitlab runner is set to use it
- [x] CI pipelines works on the branch
## TrackEmmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/128File CommandLineOptions.ixx.o missing2023-03-30T16:48:41+02:00Celine FouardFile CommandLineOptions.ixx.o missing## About you
Céline Fouard ex-CamiTK developper, now CamiTK intensive user
## Overview
I want to install CamiTK on my brand new machine (Ubuntu 22.04.2 LTS 64 bits), and I choose to install the develop version from git.
## Steps to R...## About you
Céline Fouard ex-CamiTK developper, now CamiTK intensive user
## Overview
I want to install CamiTK on my brand new machine (Ubuntu 22.04.2 LTS 64 bits), and I choose to install the develop version from git.
## Steps to Reproduce
I checkedout sources in a scr/ directory, and created a buid/ directory. Into the build, I exectued the following commands:
> cmake $CAMITK_SOURCE_DIR -DCEP_IMAGING=TRUE -DCEP_MODELING=TRUE -DCEP_TUTORIALS=TRUE -DCMAKE_INSTALL_PREFIX="/opt/camitk"
> cmake --build . --parallel 8 --target install
## Actual VS Expected Result
I obtained the following result:
## Relevant logs and/or screenshots
[Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's very hard to read otherwise.]
```[ 45%] Linking CXX executable ../../../bin/camitk-actionstatemachine
/usr/bin/ld : ne peut pas trouver CMakeFiles/application-actionstatemachine.dir/CommandLineOptions.ixx.o : Aucun fichier ou dossier de ce type
collect2: error: ld returned 1 exit status
gmake[2]: *** [sdk/applications/actionstatemachine/CMakeFiles/application-actionstatemachine.dir/build.make:503 : bin/camitk-actionstatemachine] Erreur 1
gmake[1]: *** [CMakeFiles/Makefile2:5561 : sdk/applications/actionstatemachine/CMakeFiles/application-actionstatemachine.dir/all] Erreur 2
gmake: *** [Makefile:166 : all] Erreur 2
```
## Interpretation & Possible fixes
I had the same problem compiling the camitk-5.0.2 package on with install target at /usr/local/. The actual firs error was the same error, but on the application testcomponent.
I do not understand where this come from, I did not touch my paths...
## CamiTK Version
[Copy/Paste the output of `camitk-config -b` CamiTK Version part ]
> can't run camitk-config....
---
**please do not remove anything below this line**https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/127Support of ITK5 on debian2022-11-20T10:08:49+01:00Emmanuel PromayonSupport of ITK5 on debian## About you
CamiTK developer
## Product
camitk community edition
## Overview
debian got rid of itk4, and will only support itk5 from now on.
Next ubuntu LTS has a debian freeze on February 24
## Challenge
get camitk5 back into un...## About you
CamiTK developer
## Product
camitk community edition
## Overview
debian got rid of itk4, and will only support itk5 from now on.
Next ubuntu LTS has a debian freeze on February 24
## Challenge
get camitk5 back into unstable and therefore support ITK5 and all new sid niceties and updates...Emmanuel PromayonEmmanuel Promayon2022-02-14https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/121Debian packaging failed2021-02-01T22:22:38+01:00Emmanuel PromayonDebian packaging failedJob [#197871](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871) failed for 45108ed033f366a2c065e14aae61c1fd7c83255b:
The package was not generated, please check the artifacts and fix the problem:
- summary: https...Job [#197871](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871) failed for 45108ed033f366a2c065e14aae61c1fd7c83255b:
The package was not generated, please check the artifacts and fix the problem:
- summary: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/debian-unstable-develop/log/summary.log
- check environment: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/debian-unstable-develop/log/check-environment.log
- build package: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/debian-unstable-develop/log/build-package.log
- prepare package environment: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/197871/artifacts/raw/debian-unstable-develop/log/prepare-package-environment.logCamiTK 4.2 Sprint # 3Emmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/114Failed test in action state machine2020-11-25T01:00:51+01:00Emmanuel PromayonFailed test in action state machine## About you
CamiTK developer
## Overview
Job [#178103](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/178103) failed for 92087062bc6533f58297c18826f5256436b37807
- The new action state machine test generates a bug, ...## About you
CamiTK developer
## Overview
Job [#178103](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/178103) failed for 92087062bc6533f58297c18826f5256436b37807
- The new action state machine test generates a bug, see
## Steps to Reproduce
Just check the pipeline.
On Linux (Job [#178103](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/178103)):
```
132: X Error of failed request: BadWindow (invalid Window parameter)
132: Major opcode of failed request: 2 (X_ChangeWindowAttributes)
132: Resource id in failed request: 0x2
132: Serial number of failed request: 7
132: Current serial number in output stream: 9
132: QObject::disconnect: Unexpected null parameter
```
On Windows (Job [#175675](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/175675)):
```
131: 2020-11-10 05:27:09.600 [TRACE ] Application "camitk-actionstatemachine" - Logging in C:/builds/win10-develop/sdk/applications/actionstatemachine/2020-11-10T05-27-09
131: 2020-11-10 05:27:10.760 [ERROR ] Application "camitk-actionstatemachine" - Caught an unknown exception
131: C:/builds/win10-develop/bin/camitk-actionstatemachine-debug.exe aborted...
131: Unknown Exception
1/1 Test #131: application-actionstatemachine-4 ...***Exception: SegFault 6.90 sec
```
(there is also another bug in this job, as the error is not considered failed by the pipeline)
## Actual VS Expected Result
Should not failed
## Relevant logs and/or screenshots
See related jobs
## CamiTK Version
CamiTK 4.2.dev.develop.92087062
Compiled using git Hash: 92087062bc6533f58297c18826f5256436b37807, Date: Tue Oct 20 00:24:15 2020 +0200.
---
**please do not remove anything below this line**CamiTK 4.2 Sprint # 3Emmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/115Pipeline does not detect failed tests2020-11-22T10:07:31+01:00Emmanuel PromayonPipeline does not detect failed tests## About you
CamiTK developer
## Overview
The action state machine tests failed, tests are sometimes reran, but the errors are not detected by the test script.
The pipeline does not fail although it should clearly fail. We are lull to ...## About you
CamiTK developer
## Overview
The action state machine tests failed, tests are sometimes reran, but the errors are not detected by the test script.
The pipeline does not fail although it should clearly fail. We are lull to a false sense of security, while there is a bug!
The two Linux configuration shows different logs but both do not detect the error
## Steps to Reproduce
- For linux stable: check [Job #177308](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/177308)
- For linux LTS: check [Job #177309](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/177309)
## Actual VS Expected Result
The pipeline should fail when there is a failed test, independently of the type of failure.
## Relevant logs and/or screenshots
### On Linux stable
In the [Job #177308](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/177308) log,
the initial tests failed with:
```
4/5 Test #132: application-actionstatemachine-5 .........Child aborted***Exception: 2.81 sec
5/5 Test #131: application-actionstatemachine-4 .........***Timeout 1800.13 sec
```
But then at the end of the job log we have:
```
===== Fatal errors =====
Found fatal error in /builds/CamiTK/CamiTK/debian-stable-develop/log/ci-test.log
===== Failed tests =====
===== Re-running failed tests =====
Re-ran tests OK
```
The relevant lines in the test.log show:
```
132: X Error of failed request: BadWindow (invalid Window parameter)
132: Major opcode of failed request: 2 (X_ChangeWindowAttributes)
132: Resource id in failed request: 0x2
132: Serial number of failed request: 7
132: Current serial number in output stream: 9
132: terminate called after throwing an instance of 'std::bad_array_new_length'
132: what(): std::bad_array_new_length
4/5 Test #132: application-actionstatemachine-5 .........Child aborted***Exception: 2.81 sec
5/5 Test #131: application-actionstatemachine-4 .........***Timeout 1800.13 sec
```
The rerun-test.log contains only one line:
```
Checking /builds/CamiTK/CamiTK/debian-stable-develop/log/test.log for failed test
```
### On Linux LTS
In the [Job #177309](https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/jobs/177309) log,
the initial tests failed with:
```
4/5 Test #131: application-actionstatemachine-4 .........Child aborted***Exception: 0.71 sec
5/5 Test #132: application-actionstatemachine-5 .........***Timeout 1800.13 sec
```
But then at the end of the job log we have:
```
===== Fatal errors =====
Found fatal error in /builds/CamiTK/CamiTK/ubuntu-lts-develop/log/ci-test.log
===== Failed tests =====
===== Re-running failed tests =====
Re-ran tests OK
```
The relevant lines in the test.log show:
```
131: ...
131: X Error of failed request: BadWindow (invalid Window parameter)
131: Major opcode of failed request: 2 (X_ChangeWindowAttributes)
131: Resource id in failed request: 0x2
131: Serial number of failed request: 7
131: Current serial number in output stream: 9
131: terminate called after throwing an instance of 'std::bad_alloc'
131: what(): std::bad_alloc
4/5 Test #131: application-actionstatemachine-4 .........Child aborted***Exception: 0.71 sec
5/5 Test #132: application-actionstatemachine-5 .........***Timeout 1800.13 sec
```
The rerun-test.log contains only one line:
```
Checking /builds/CamiTK/CamiTK/ubuntu-lts-develop/log/test.log for failed test
```
## Interpretation & Possible fixes
The test script is faulty, see `.gitlab/test.sh`.
It should be better at parsing the log to detect problems
## CamiTK Version
CamiTK 4.2.dev.develop.92087062
Compiled using git Hash: 92087062bc6533f58297c18826f5256436b37807, Date: Tue Oct 20 00:24:15 2020 +0200.CamiTK 4.2 Sprint # 3Emmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/104Update CI for packaging2020-07-06T22:48:00+02:00Emmanuel PromayonUpdate CI for packaging| | |
|--|--|
| **As a** | CamiTK developer |
| **I would like to** | test debian sid compilation of develop |
| **So that** | quickly be able to produce an official debian packaging |
| **Epic/Topics** | /label ~"Track Continuous Integ...| | |
|--|--|
| **As a** | CamiTK developer |
| **I would like to** | test debian sid compilation of develop |
| **So that** | quickly be able to produce an official debian packaging |
| **Epic/Topics** | /label ~"Track Continuous Integration" |
## Description / Overview
Considering:
- the change in the VM server at TIMC (note: domain is now `u-ga.fr` not `imag.fr`)
- the update policy for supported dependencies and toolchain (see #96)
The packaging should work on the current develop branch
## Hints
- Check packaging pipeline logs
- Update code or CMake accordingly
## Acceptance tests
- [x] `camitk-ci-linux-packaging` host the updated packaging CI gitlab runner
- [x] the packaging pipeline is back working
## Track
/label ~"Track Continuous Integration" CamiTK 4.2 Sprint # 2Emmanuel PromayonEmmanuel Promayonhttps://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/issues/4ctest build name should be set before ctest start2018-03-14T14:08:54+01:00Emmanuel Promayonctest build name should be set before ctest startIf `CTEST_BUILD_NAME` is not set before `ctest_start` the build name that appears on the dashboard is `(empty)`.
The problem is to have the proper hash *before* `ctest_update` is called. As `ctest_update` is called *after* `ctest_start`,...If `CTEST_BUILD_NAME` is not set before `ctest_start` the build name that appears on the dashboard is `(empty)`.
The problem is to have the proper hash *before* `ctest_update` is called. As `ctest_update` is called *after* `ctest_start`, one need to get the hash from origin.Sprint 5Emmanuel PromayonEmmanuel Promayon