Add packages for tools chapter

[Zethson]

Check whether scvi-tools isn't part of the container yet. Thought it should be already...

[Zethson]

@le-ander the container is now building for 3.5 hours already. I thought that we had below 1 hour (also when checking the latest successful runs). Got any idea about what is happening here?

[Zethson]

All right, this is pip being stupid and checking an ungodly amount of compatible versions. Mhmm, what can we do about it?

[le-ander]

oh, looks like we have some serious requirement crashes here. have never seen this before tbh

[Zethson]

@le-ander I "hacked" pip which may or may not cause downstream issues.

However, now I get

Step 19/49 : RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')"
 ---> Running in 87e77d78fa3c
Error: Bioconductor version '3.14' requires R version '4.1'; see
  https://bioconductor.org/install
Execution halted
The command '/bin/sh -c Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')"' returned a non-zero code: 1

which is not related to the Python packages. Do we need to force some version constraint somewhere here to solve this?

[le-ander]

interesting.
looks like you get r-base-core 4.2.0-1~bullseyecran.0 when installing r-base-dev=4.1.2-1~bullseyecran.0

[le-ander]

Okay, pinning R versions does not seem to work when using apt installs of packages:

Step 18/50 : RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel r-cran-lme4
 ---> Running in 7399a402b8d8
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-cran-lattice : Depends: r-base-core (>= 4.2.0-1~bullseyecran.0) but 4.1.2-1~bullseyecran.0 is to be installed
 r-cran-mass : Depends: r-base-core (>= 4.2.0-1~bullseyecran.0) but 4.1.2-1~bullseyecran.0 is to be installed
 r-cran-matrix : Depends: r-base-core (>= 4.2.0-1~bullseyecran.0) but 4.1.2-1~bullseyecran.0 is to be installed
 r-cran-nlme : Depends: r-base-core (>= 4.2.0-1~bullseyecran.0) but 4.1.2-1~bullseyecran.0 is to be installed
 r-cran-rcpp : Depends: littler
               Depends: r-cran-littler but it is not installable
E: Unable to correct problems, you have held broken packages.
The command '/bin/sh -c apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel r-cran-lme4' returned a non-zero code: 100

Error: Process completed with exit code 100.

As installing all packages from source requires a LOT more CPU time, I'd say we just stick with the latest R version in these builds and adapt the biocmanager accordingly.

[le-ander]

@Zethson all fixed :)

[Zethson]

Thanks. I'll need to check the container first to see whether I broke the Python environment....