upgrade base ubuntu 22 + common sdist output file name fix

[davidsmejia]

Issue Number

#3573

Purpose/Implementation Notes

This pull request updates the base Docker image and build process for the project, modernizing the environment and improving compatibility with newer system libraries and Python/R dependencies. The most significant changes are the upgrade from Ubuntu 18.04 to 22.04, a complete overhaul of the system package installation process, and a new approach to building and installing R 3.4.4 and Bioconductor dependencies. Additionally, there are adjustments to how the shared Python package is copied into various Docker images to handle special characters in filenames.

Base image and build environment modernization:

• Upgraded the base image in common/dockerfiles/Dockerfile.base from ubuntu:18.04 to ubuntu:22.04, and removed the use of MIT mirror for apt sources.
• Overhauled system package installation: removed PPAs and apt-fast, updated to newer library versions (e.g., llvm-14-dev), added required development libraries for R and Python, and adjusted Python and pip installation steps for compatibility with Ubuntu 22.04.
• Added steps to build R 3.4.4 from source with modern compiler flags to ensure compatibility with the newer GCC and system libraries, and pre-installed Bioconductor's BiocInstaller to work around deprecated bootstrap URLs.

Python shared package installation:

• Updated all Dockerfiles to use a COPY pattern that replaces dashes with question marks (data?refinery?common-*) when copying the shared data-refinery-common Python wheel, ensuring compatibility with shell globbing and special character handling in filenames. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10]

Methods

N/A

Types of changes

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)

Functional tests

Local builds

Checklist

• Lint and unit tests pass locally with my changes

Screenshots

N/A