Update tool-Docker-action to v2.1.0

[nwiltsie]

This PR updates the tool-Docker-action Action to version 2.1.0. There are a few big changes in this version:

1. Pushing to any branch foo will build this repository's image and tag it as branch-foo. That tagged image will be removed when the branch is deleted.
2. By default the Action will only build SemVer tags (e.g. v1.2.3-xxx). Repositories that need to use other kinds of tags (e.g. v1.2beta) can pass the optional non-semver-tags argument; doing so will build all tags that begin with v.

There are a bunch of smaller changes buried in there - you can see them all at this link.

Based on this repository's existing tags, I've determined that it does follow semantic versioning. The updated workflow therefore does not pass the non-semver-tags argument to the Action, although it can be uncommented in the future if need be.

[Faizal-Eeman]

Looks good!

[nwiltsie]

Something's wonky here - the image isn't building correctly in this branch or on main. See #22.

[wiz-inc-8da00b022c]

Wiz Scan Summary

IaC Misconfigurations
Vulnerabilities
Sensitive Data
Total
Secrets

[nwiltsie]

Okay @Faizal-Eeman, I think that I've got the build repaired.

1. I switched the base image from r-base to rocker/r-ver because the former is not version-pinned (see Docker image r-base:4.2.1 not reproducible rocker-org/rocker#540 (comment)).
2. r-base installs R into /usr/lib while r-ver installs it into /usr/local/lib, so I messed with the library logic (a0c4bc4) and it seems to work now.

Sanity-checking that, the install.packages command installs into /usr/local/lib/R/site-library...:

0.394 > install.packages(c("argparse", "BiocManager", "pkgdepends", "optparse"))
0.397 Installing packages into ‘/usr/local/lib/R/site-library’
0.397 (as ‘lib’ is unspecified)

So does the BiocManager::install command (I added some bold emphasis):

18.00 Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)
18.00 Installing package(s) 'BiocVersion', 'ellipsis', 'VariantAnnotation'
18.34 also installing the dependencies ‘formatR’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘sys’, ‘lambda.r’, ‘futile.options’, ‘bit’, ‘vctrs’, ‘cachem’, ‘askpass’, ‘abind’, ‘SparseArray’, ‘futile.logger’, ‘snow’, ‘BH’, ‘cpp11’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘plogr’, ‘png’, ‘mime’, ‘openssl’, ‘RCurl’, ‘rjson’, ‘yaml’, ‘matrixStats’, ‘UCSC.utils’, ‘GenomeInfoDbData’, ‘S4Arrays’, ‘DelayedArray’, ‘bitops’, ‘BiocParallel’, ‘crayon’, ‘RSQLite’, ‘KEGGREST’, ‘XML’, ‘httr’, ‘GenomicAlignments’, ‘BiocIO’, ‘restfulr’, ‘rlang’, ‘BiocGenerics’, ‘MatrixGenerics’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’, ‘DBI’, ‘zlibbioc’, ‘Biobase’, ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘Biostrings’, ‘AnnotationDbi’, ‘rtracklayer’, ‘BSgenome’, ‘GenomicFeatures’, ‘Rhtslib’

62.18 * installing source package ‘zlibbioc’ ...
62.18 ** using staged installation
62.52 configure: creating ./config.status
62.60 config.status: creating src/Makevars
62.64 ** libs
62.65 using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
62.65 mkdir -p "/usr/local/lib/R/site-library/00LOCK-zlibbioc/00new/zlibbioc/include"
62.66 gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_zlibbioc.c -o R_init_zlibbioc.o
62.67 gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o zlibbioc.so R_init_zlibbioc.o -L/usr/local/lib/R/lib -lR
62.68 installing to /usr/local/lib/R/site-library/00LOCK-zlibbioc/00new/zlibbioc/libs

The installer.R logs don't report the installation path, but the docker image itself shows that Battenberg was installed to /usr/local/lib/R/site-library:

$ docker run -it ghcr.io/uclahs-cds/battenberg:branch-nwiltsie_update_docker_action ls -1 /usr/local/lib/R/site-library/Battenberg
DESCRIPTION
example
extdata
help
html
INDEX
LICENSE
Meta
NAMESPACE
R
TODO

[Faizal-Eeman]

The installer.R logs don't report the installation path, but the docker image itself shows that Battenberg was installed to /usr/local/lib/R/site-library:
docker run -it ghcr.io/uclahs-cds/battenberg:branch-nwiltsie_update_docker_action ls -1 /usr/local/lib/R/site-library/Battenberg

Yup, tested the above command and confirming Battenberg is available in /usr/local/lib/R/site-library

[Faizal-Eeman]

Thanks a lot @nwiltsie. I'm merging this PR.