Hi, hard to give you specific tipps for your own extensions but typically there are two reasons that lead to missing binaries in packages:
(1) The dependencies could not be found because they are not located in the search paths (2) You do either not link during link-time to the dependencies but dynamically in runtime either directly or indirectly because of the plugin architecture. As far as I know CPack crawls the executables low-level to figure out their true dependencies. As soon as it found a link to VMTK for example it is supposed to add the VMTK libraries to the package. There’s one place in the whole packaging script where we tell CPack/Cmake about the executables and the plugins as they are no link-time dependencies of the executables. I’m not sure about (1) as on macOS dependencies tend to be written in absolute paths in the binaries. You can easily check the depednencies with the otool (-L parameter). Usually you’ll get an idea whats going on especially when comparing your packaged binaries with the build-tree binaries. Besides all that, I would recommend to perform the install step of VMTK in the superbuild. We already set the install path of all external projects to the ep folder. If VMTK does not provide the typical Targets.cmake file you still have the PackageConfig files in CMake/PackageDepends to set things up and/or the possibility to add a FindVMTK.cmake file to the CMake folder. From: José Alonso Solís Lemus [mailto:alonso.j...@gmail.com] Sent: Tuesday, June 25, 2019 2:01 PM To: Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de> Cc: mitk-users@lists.sourceforge.net Subject: Re: [mitk-users] [Migrating to MITK v2018.04.2] Problems with external applications Dear all, We are experiencing a problem packaging our application in macOS. First, let me provide some context. We are implementing our application running as an external project over an MITK build (2018.04.2), we followed the Extension project template and through recent time and help from this mailing list, we managed to make our project compile in both ubuntu and macOS. We are also using an external project (VMTK), which is cloned and built into the ep/src successfully. The problem we are running into comes when packaging, i.e running a make package in the MITK-build directory. Everything seems to be linked and copied correctly, except for our external project VMTK. I'll first get errors regarding libraries not being copied correctly, and when actually trying to link the files, we get the bigger error that stops the packaging: 208/530: copying '@rpath/libvtkvmtkComputationalGeometry.dylib' Error copying file "@rpath/libvtkvmtkComputationalGeometry.dylib" to "/path/to/mitk-super/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2018.04.2-local_changes-macos-x86_64/MitkMainApp.app/Contents/MacOS/libvtkvmtkComputationalGeometry.dylib". ... ... error: /Library/Developer/CommandLineTools/usr/bin/install_name_tool: can't open file: /path/to/mitk-super/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2018.04.2-local_changes-macos-x86_64/MitkMainApp.app/Contents/MacOS/libvtkvmtkCommon.dylib (No such file or directory) CMake Error at /path/to/mitk-src/CMake/BundleUtilities.cmake:883 (message): Command failed: 'install_name_tool' '-id' '@executable_path/../MacOS/libvtkvmtkCommon.dylib' '/path/to/mitk-super/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2018.04.2-local_changes-macos-x86_64/MitkMainApp.app/Contents/MacOS/libvtkvmtkCommon.dylib' I have two hypotheses as to why this is happening and how to fix it: First: VMTK does not have an install target built, therefore it is not possible to do a make install, and its libraries are not being copied into the ep/lib/ folder. Second: I remember the FixMacOSInstaller.cmake file, which is not linking any of the libraries from the external projects. I thought I could add something there.. but I'm not sure how. I wonder if (in the meantime) it would suffice to copy VMTK's libraries (which are properly being generated) into the ep/lib folder. Any ideas? Thank you very much for your time, looking forward to your answer. Kind regards, José Alonso On Wed, 5 Jun 2019 at 09:07, Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> wrote: Thank you! We plan to add an example app in near future to the project template and your input will probably save us quite some time. :-) Regarding the shortlinks it is a dirty workaround for now as far as I remember. The thing is, there shouldn’t be a compile-time or link-time dependence to any autoload module, making the autoloading pretty much pointless, right? However, we didn’t notice we have one of such a dependency last minute before the actual release and it only showed up on macOs so we decided to work around this by creating symlinks to autoload modules beside the application executable until the affected module is restructured accordingly. We also run into the CMake warning regarding CMP0042 but as far as I can tell it doesn’t lead to any issues. Best, Stefan From: José Alonso Solís Lemus [mailto:alonso.j...@gmail.com<mailto:alonso.j...@gmail.com>] Sent: Tuesday, June 4, 2019 4:46 PM To: Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> Cc: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: Re: [mitk-users] [Migrating to MITK v2018.04.2] Problems with external applications Hi all! Regarding the ID issue, I did three things on the Applications/CMakeLists.txt in my project folder. (For context, I have a variable called MY_APP_NAME, which I'll reference in the text below: 1. Removed the _plugins variable. Before I would have only the plugins I thought I needed for our project, I removed it in favour of building all MITK plugins. I added a variable _exclude_plugins which I add to the mitkFunctionCreateBlueBerryApplication macro. The excluded plugins are exactly the same as the ones set in the Workbench. 2. Added the meta-dependencies. if(TARGET ${CMAKE_PROJECT_NAME}-autoload) add_dependencies(${MY_APP_NAME} ${CMAKE_PROJECT_NAME}-autoload) endif() 3. Added a build time dependency to legacy BlueBerry bundles. if(MITK_MODULES_ENABLED_PLUGINS) add_dependencies(${MY_APP_NAME} ${MITK_MODULES_ENABLED_PLUGINS}) endif() After that, it all seemed to work! If it still doesn't make sense for you, I'm happy to have a look into my git changes, but I'm 95% sure I did nothing outside these three aspects. Regarding the macOS installation, thank you for the hint. I'll try digging to see what can find, the only difference I see is some symlinks being created. Although, you did make me question whether I have the right MITK tag (I think I have a different one on the Mac than on linux, so I'll check). The problem I'm seeing is that I see no error or flag being raised. The MITK build seems to work perfectly fine, but at the end of the make command, I do not see the "[100%] Built target MyApp" I would expect to see and of course, the MITK-build/bin folder does not have MyApp anywhere. The only thing that seems different is when running make, just after the summary of all modules being built, I get the following: CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning. MACOSX_RPATH is not specified for the following targets: CppMicroServices TestModuleA TestModuleA2 TestModuleAL TestModuleAL2 TestModuleAL2_1 TestModuleAL_1 TestModuleB TestModuleH TestModuleM TestModuleR TestModuleRA TestModuleRL TestModuleS TestModuleSL1 TestModuleSL3 TestModuleSL4 mymodule This warning is for project developers. Use -Wno-dev to suppress it. Do you think this is related? I have no idea how to fix this. In fact, I think MITK already addresses this? Will keep in touch :) Kind regards, José Alonso On Tue, 4 Jun 2019 at 13:26, Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> wrote: Hi, good to hear. Do you have any hints on the missing ID issue? Regarding macOS packaging, well, it’s complicated and we would need specific information on what is going wrong. Getting our packaging script right on macOS was a little nightmare and we still have a custom fix script after the actual packaging to get things working (maybe that’s already a good hint): https://github.com/MITK/MITK/blob/v2018.04.2/CMake/FixMacOSInstaller.cmake Best, Stefan From: José Alonso Solís Lemus [mailto:alonso.j...@gmail.com<mailto:alonso.j...@gmail.com>] Sent: Tuesday, June 4, 2019 12:59 PM To: Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> Cc: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: Re: [mitk-users] [Migrating to MITK v2018.04.2] Problems with external applications Hello! I've managed to compile properly the project properly by following both the Diffusion app and the Workbench. It works well on Ubuntu, even the packaging. Now our focus is building the app for macOS. We have managed to make the project compile, however our app is not being packaged properly. Do you have any ideas? Kind regards, José Alonso On Fri, 24 May 2019 at 20:02, José Alonso Solís Lemus <alonso.j...@gmail.com<mailto:alonso.j...@gmail.com>> wrote: Hello! Thank you for your reply. I started following the Workbench. I got it to work (compiled+running), it is now not "finding the editor". I followed both the Workbench and the Diffusion app. I'll be happy to give more information as needed. So if I get it to work, I'll reply back to this thread. Thank you for confirming I'm on the right track! Kind regards, José Alonso On Fri, 24 May 2019 at 16:45, Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> wrote: Hi Jose, recently two colleagues stumbled upon the same id problem. One person started from the Diffusion app as an example and run into the problem, the second person did it as well at the same time but it worked and they continued with that version then. It possibly will take a few days but we try to identify the difference and may give you an answer. Please tell us if you figure it out by yourself, though. :) From: José Alonso Solís Lemus [mailto:alonso.jasl+...@gmail.com<mailto:alonso.jasl%2b...@gmail.com>] Sent: Thursday, May 23, 2019 4:01 PM To: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: [mitk-users] [Migrating to MITK v2018.04.2] Problems with external applications Dear MITKers, Thank you very much for your help so far. We have other inquiries regarding the upgrade of our app. For context, I'll repeat some of the things I've said already in this thread. We are in the process of migrating our application from v2016.03 to v2018.04.2, following the external project template. We used to have an application, for which in the 2016 build would have its Apps directory, which we took from the external project template in v2016. Right now, we got the MITK build to compile with our external Modules and Plugins, some of them even come through nicely in the Workbench. However, as mentioned before, we used to have a standalone app developed. The external projects template only includes examples for modules, plugins and command line applications. I looked through the ./CMakeLists.txt and noticed that it is possible to have an Applications folder, so I tried adapting our original Apps directory into an Applications, following roughly the Applications folder in the MITK source. The whole MITK build finishes successfully, however, when trying to run it, we get an error message, which in summary shows the following: 0.325! WARNING: Application launch failed: Application Exception: No application id has been found. ... !0.325! WARNING: Startup error: Application Exception: No application id has been found. ... Segmentation fault (core dumped) Perhaps a problem with libMitkAppUtil, of some of the CTK libraries? I'm not sure. I'm pasting the full error message at the bottom of this. Specifically, if we're aiming to produce a standalone application in which our developments can then be later be packaged into binaries, do we need to do something extra that is not in the External Project Template? Is there a place we could check how to make it work or perhaps a checklist of places we could try looking into? I hope I explained the problem well, please ask any questions you might still have. Looking forward to your response. Kind regards, Jose Alonso Full error: 0.325! WARNING: Application launch failed: Application Exception: No application id has been found. at 0x7f9fe1830837: ??? + 0xe1830837 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKCore.so.0.1 at 0x7f9fe18303a1: ctkBackTrace::ctkBackTrace(unsigned long) + 0xd3 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKCore.so.0.1 at 0x7f9fe18594af: ctkException::ctkException(QString const&) + 0x49 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKCore.so.0.1 at 0x7f9fe8a723c7: ctkApplicationException::ctkApplicationException(int, QString const&) + 0x35 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fc4ba538b: ??? + 0xc4ba538b in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/plugins/liborg_blueberry_core_runtime.so at 0x7f9fc4c11287: ??? + 0xc4c11287 in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/plugins/liborg_blueberry_core_runtime.so at 0x7f9fe8a004e7: ??? + 0xe8a004e7 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe89ffd80: ??? + 0xe89ffd80 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe8a3307a: ctkPluginFrameworkLauncher::run(QVariant const&) + 0x2f6 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe8a32981: ctkPluginFrameworkLauncher::run(QRunnable*, QVariant const&) + 0x159 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe9db79d1: mitk::BaseApplication::main(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) + 0x15d in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/libMitkAppUtil.so at 0x7f9fe87848ae: Poco::Util::Application::run() + 0x6a in /home/jsl19/dev/mitk-cemrg/ep/lib/libPocoUtild.so.60 at 0x7f9fe9dba7f4: mitk::BaseApplication::run() + 0x64 in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/libMitkAppUtil.so at 0x401130: ??? + 0x401130 in ./MITK-build/bin/CemrgApp at 0x7f9fe8ccd830: __libc_start_main + 0xf0 in /lib/x86_64-linux-gnu/libc.so.6 at 0x400f39: ??? + 0x400f39 in ./MITK-build/bin/CemrgApp !0.325! WARNING: Startup error: Application Exception: No application id has been found. at 0x7f9fe1830837: ??? + 0xe1830837 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKCore.so.0.1 at 0x7f9fe18303a1: ctkBackTrace::ctkBackTrace(unsigned long) + 0xd3 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKCore.so.0.1 at 0x7f9fe18594af: ctkException::ctkException(QString const&) + 0x49 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKCore.so.0.1 at 0x7f9fe8a723c7: ctkApplicationException::ctkApplicationException(int, QString const&) + 0x35 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fc4ba538b: ??? + 0xc4ba538b in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/plugins/liborg_blueberry_core_runtime.so at 0x7f9fc4c11287: ??? + 0xc4c11287 in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/plugins/liborg_blueberry_core_runtime.so at 0x7f9fe8a004e7: ??? + 0xe8a004e7 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe89ffd80: ??? + 0xe89ffd80 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe8a3307a: ctkPluginFrameworkLauncher::run(QVariant const&) + 0x2f6 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe8a32981: ctkPluginFrameworkLauncher::run(QRunnable*, QVariant const&) + 0x159 in /home/jsl19/dev/mitk-cemrg/ep/src/CTK-build/CTK-build/bin/libCTKPluginFramework.so.0.1 at 0x7f9fe9db79d1: mitk::BaseApplication::main(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) + 0x15d in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/libMitkAppUtil.so at 0x7f9fe87848ae: Poco::Util::Application::run() + 0x6a in /home/jsl19/dev/mitk-cemrg/ep/lib/libPocoUtild.so.60 at 0x7f9fe9dba7f4: mitk::BaseApplication::run() + 0x64 in /home/jsl19/dev/mitk-cemrg/MITK-build/lib/libMitkAppUtil.so at 0x401130: ??? + 0x401130 in ./MITK-build/bin/CemrgApp at 0x7f9fe8ccd830: __libc_start_main + 0xf0 in /lib/x86_64-linux-gnu/libc.so.6 at 0x400f39: ??? + 0x400f39 in ./MITK-build/bin/CemrgApp Segmentation fault (core dumped) -- - José Alonso Solís Lemus - -- - José Alonso Solís Lemus - -- - José Alonso Solís Lemus - -- - José Alonso Solís Lemus -
_______________________________________________ mitk-users mailing list mitk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mitk-users
