Update to R version 4.2.3 in docker image

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update Dockerfile

What was your approach?

• to rocker tidyverse:4.2.3
• Include vroom R package

What GitHub issue does your pull request address?

• Update to R version 4.2.3 in docker image  ticket-tracker-OPC#537
• Add vroom to docker image after v12 ticket-tracker-OPC#515

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

All module in CI testing passing GitHub Action

Is there anything that you want to discuss further?

NA

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

YES

Results

What types of results are included (e.g., table, figure)?

NA

What is your summary of the results?

NA

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

Hey @ewafula for the modules with code changes, can you rerun those fully to make sure no results change?

[ewafula]

Hey @ewafula for the modules with code changes, can you rerun those fully to make sure no results change?

@jharenza, the major updates had to do with docker dependencies. Logically the three modules update would have no effect.

• TP53 module update:
  • the latest version of the rpy2 python3 package that can install on Ubuntu jammy has a change in the module-method name for loading RDS files from pandas2ri.ri2py (v2.9.3) to pandas2ri.rpy2py(v3.5.0). This does not affect results.
  • the installation rpy2 package (>=v3.0.0) on Ubuntu jammy does load the R is a shared library (libR.so) when imported in python scripts. This is a known issue by the rpy2 developers, and the recommended solution is setting the environmental variable LD_LIBRARY_PATH pointing to the R system installation in the user's .bashrc/.bash_profile file. That is not easy to implement in docker instances. Therefore, I am setting these in the module bash script. This also does not affect results.

    export R_HOME='/usr/local/lib/R'
    export LD_LIBRARY_PATH=${R_HOME}/lib:${LD_LIBRARY_PATH}
    

• TPM summary stats and fusion freq module updates:
  • the latest version of dplyr that is built for R >=4.0.0 check for strict typing. Don't allow mutating between variable two different class variables. These are the only ones addressed to avoid column class conflicts and do not affect results.

  error in `na_if()`: ! Can't convert `y` <character> to match type of `x` <double>
  error in `mutate()`: ! Can't convert `y` <character> to match type of `x` <logical> 
  

I can rebuild the image on ec2 and rerun these three modules if you still want me to.

[jharenza]

How about stacking the reruns on this PR? We need to rerun anything with a code change. - looks like fusion filtering and tpm stats?