Rokita/update dockerfile

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR updates the dockerfile to R 4.4.0 and uses BioC 3.19 to source any R packages not on GitHub so that they are compatible with R 4.4.0

What was your approach?

Updated dockerfile and pushed to CAVATICA at pgc-images.sbgenomics.com/d3b-bixu/pbta-ancestry:latest

What GitHub issue does your pull request address?

Closes #69

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

soliciting.

Which areas should receive a particularly close look?

There is one script 03-plot-survival.R with an error, due to a str_replace in the plotting function:

Rscript --vanilla 03-plot-survival.R
-- Attaching core tidyverse packages ---------------------------------------------------------- tidyverse 2.0.0 --
v dplyr     1.1.4     v readr     2.1.5
v forcats   1.0.0     v stringr   1.5.1
v ggplot2   3.5.1     v tibble    3.2.1
v lubridate 1.9.3     v tidyr     1.3.1
v purrr     1.0.2     
-- Conflicts ---------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
i Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Loading required package: colorspace
Loading required package: ggpubr

Attaching package: 'survminer'

The following object is masked from 'package:survival':

    myeloma

Rows: 1485 Columns: 41
-- Column specification ------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (22): Kids_First_Biospecimen_ID, predicted_ancestry, Kids_First_Particip...
dbl (18): EAS_prob, AFR_prob, AMR_prob, SAS_prob, EUR_prob, PC1, PC2, PC3, P...
lgl  (1): given_ancestry

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in `dplyr::mutate()`:
i In argument: `term_display = str_replace(...)`.
Caused by error in `str_replace()`:
! `pattern` can't be the empty string (`""`).
Backtrace:
     x
  1. +-global plotForest(os_survival_result)
  2. | \-... %>% ...
  3. +-dplyr::mutate(., term_display = fct_relevel(term_display, unique(term_display)))
  4. +-dplyr::mutate(...)
  5. +-dplyr:::mutate.data.frame(...)
  6. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. |   +-base::withCallingHandlers(...)
  8. |   \-dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. |     \-mask$eval_all_mutate(quo)
 10. |       \-dplyr (local) eval()
 11. +-stringr::str_replace(...)
 12. | \-stringr:::check_lengths(string, pattern, replacement)
 13. |   \-vctrs::vec_size_common(...)
 14. \-stringr::str_replace(term, paste(names(model$xlevels), collapse = "|"), "")
 15.   \-stringr:::no_empty()
 16.     \-cli::cli_abort(...)
 17.       \-rlang::abort(...)
There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Is there anything that you want to discuss further?

Yes, we should make sure we fix the plotting issue - pull using:
docker pull pgc-images.sbgenomics.com/d3b-bixu/pbta-ancestry:latest

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)?

What is your summary of the results?

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]

side note: I noticed heatmap_function.R is duplicated in braf-fusions and survival - only need one, but maybe you took care of that with your update in #61

[rjcorb]

runs successfully after merging latest approved PR which updated plotting functions.