Issue Installing OsteoBioR

[arunge]

Via e-mail:

I was trying to install the offline R version of OsteoBioR on my laptop ... . However, by following instructions that are published online in github, this was not working.

@CarloCocozza As written per e-mail, please let me know some more details:

• operation system you used
• R version

• Did you try the docker installation also? (Instructions are currently given for e.g. the iso-app. You can follow the instructions analogously, after installing docker, only replace the package name in the commands, that is:

  • docker pull ghcr.io/pandora-isomemo/osteo-bior:main and
  • docker run -p 3838:3838 ghcr.io/pandora-isomemo/osteo-bior:main, and now you can access the app locally via your web browser at http://0.0.0.0:3838

  Did you try this? If not, could you do so please? OsteoBioR needs compilation of C/C++/Fortran, this can cause issues on different operating systems. The best would be to use docker here. Than, we have a controlled container that has all required dependencies.

In general, in case of installation issues, best would be always to provide:

• All commands that led to the installation error:
• The full output of sessionInfo()
• The output of options("repos")

Note: @jan-abel-inwt is currently working on filling the wikis of all apps with respective installation instructions (for docker and the R packages). However, this is not finished yet. Thank you for your patience!

[CarloCocozza]

@arunge

I copy paste here my email:

"Dear Antonia,

thanks for your email!

-I use Windows 64bit. -R versioin 4.2.2

• The message I receive is (translated): "Warning: you cannot access the index for the repository https://Pandora-IsoMemo.github.io/drat/bin/windows/contrib/4.2: it is not possible to open URL 'https://Pandora-IsoMemo.github.io/drat/bin/windows/contrib/4.2/PACKAGES' The package is available only in source form and requires compilation of C/C++/Fortran code: 'OsteoBioR' These will not be installed"

I had the same issue with MpiIsoApp. Whereas it worked properly with ReSources.

All the best,"

I just downloaded Docker, but I receive this message in the home page on my desktop app: "Docker Desktop failed to start..." What should I do?

[arunge]

@CarloCocozza Did the installation of docker on windows succeed?

[CarloCocozza]

@arunge I think it says I need to install a Linux Kernel, but I don't understand why. Probably I did need to tick on WSL 2 during the installation.

I will be out of office for a couple of hours. I can try this again at lunch time.

[arunge]

@CarloCocozza Yes, our IT said that you need to install the Linux Kernel in order to make docker run. Yes, please try to "tick on WSL 2". More details on this can be found in https://learn.microsoft.com/en-us/windows/wsl/install#install-wsl-command. (Below there is a guide on how to change the default Linux distribution, this is not necessary in our case, the default is fine.)

Please let me know, which steps you did and if it succeeded! Thanks!

[CarloCocozza]

@arunge I installed the Linux Kernel but some error occurred and now the Docker says Docker Desktop Stopped...

[arunge]

@CarloCocozza, did you already try to restart the PC? That could already help to fix the issue since the installation of WSL might require docker to restart also. It may also help to rerun the docker installation and to restart again.

If that doesn't help, we could check @isomemo how we could provide support here. We do have internal IT support, but our capacity is limited and it might be worth thinking of a solution together with MPI IT service desk. E.g. we could present the installation procedure for what is needed to get the apps to work with your service desk so that they are familiar with the use case. Then, they provide on-site support in such cases. What do you think?

[CarloCocozza]

@arunge Ok, by restarting my laptop Docker works. But I don't understand where can I write the command.

[arunge]

Commands like docker pull ghcr.io/pandora-isomemo/osteo-bior:main can be put into the windows PowerShell.

[CarloCocozza]

@arunge I followed the steps you wrote above, but the http://0.0.0.0:3838/ page is not opening. It says that the webpage might be temporary not available or permanently moved to a new address.

[isomemo]

@CarloCocozza

See if this address works:

http://127.0.0.1:3838/

[CarloCocozza]

@arunge Yes it works! So now, when I want to use it offline, I just need to input this address in the google bar? even without wifi connection?

[arunge]

@CarloCocozza Almostly. Of course, after e.g. restarting the computer you always must execute first: docker run -p 3838:3838 ghcr.io/pandora-isomemo/osteo-bior:main, then you can put http://127.0.0.1:3838/ into your browser.

To set up an app with: docker pull ghcr.io/pandora-isomemo/osteo-bior:main you will always need an internet connection.

But to start the app with: docker run -p 3838:3838 ghcr.io/pandora-isomemo/osteo-bior:main you do not net an internet connection.

[CarloCocozza]

@arunge I see, thanks!

I also installed iso-app, but when I click on http://127.0.0.1:3838/ I still get to OsteoBioR. Does Iso-app have a different address?

[arunge]

You always need to run the respective docker run command before starting another app:

docker run -p 3838:3838 http://ghcr.io/pandora-isomemo/<NAME_OF_REPOSITORY>:main

Please use the correct repository name for <NAME_OF_REPOSITORY>, e.g. "osteo-bior" or "iso-app"

[arunge]

In a similar way you can also install all the other apps locally. You only need to use the correct name of the app's github repository:

• to install (with internet connection): docker pull ghcr.io/pandora-isomemo/<NAME_OF_REPOSITORY>:main

• to run locally: docker run -p 3838:3838 ghcr.io/pandora-isomemo/<NAME_OF_REPOSITORY>:main

We are updating the respective wikis currently.

@CarloCocozza Is there any open question here, or can I close this issue?

[CarloCocozza]

@arunge I used this command: docker run -p 3838:3838 ghcr.io/pandora-isomemo/iso-app:main

and I received this error: docker: Error response from daemon: driver failed programming external connectivity on endpoint focused_thompson (95be962aef7fc60921228cc8f875cd1753f6d1058d13bbb98089033be2a7ec28): Bind for 0.0.0.0:3838 failed: port is already allocated.

[arunge]

Than there is an app still running and the port is blocked. You must halt the execution of docker in the PowerShell. In Linux one can do this with Ctrl+C or by closing the terminal.

[CarloCocozza]

@arunge I tried both by closing docker, shell and browser, or by Ctrl+C. In both cases I receive still the same error and the address only takes me to OsteoBioR

[arunge]

@isomemo Do you know how to switch between apps using the windows powerShell or the windows shell (cmd.exe)? I am using the terminal in linux and there is no such issue, I only need Ctrl+C to stop running the previous app.

[arunge]

@CarloCocozza @isomemo In case the above error occurs

docker: Error response from daemon: driver failed ... Bind for 0.0.0.0:3838 failed: port is already allocated.

one must stop the container that is still running. This can be done as follows:

1. Check which container is running with: docker ps
2. Stop the container using exactly the id from above (here ab2a252f9269): docker stop <YOUR_ID>
3. Remove the container using exactly the id from above: docker rm <YOUR_ID>
4. Check if no container is running anymore: docker ps The table should be empty now:

Now, one can start a new container, e.g. with docker run -p 3838:3838 ghcr.io/pandora-isomemo/osteo-bior:main

@jan-abel-inwt We should add the case that a port is already in use to the instructions.

[arunge]

By following the above instructions it is not possible to start two containers at the same time. There are options to do so, but those are a bit technical and one must take care of setting new ports in the correct way for each additional container.

[isomemo]

@arunge waiting on the script options as we discussed

[arunge]

There is a ticket for the scripts task:

• https://github.com/Pandora-IsoMemo/docs/issues/10