[BUG] unknown instruction error when adding commands in CRAN builds

[munishchouhan]

Getting error when providing command in CRAN build

2026-01-13 06:36:31.409 | #1 [internal] load build definition from Containerfile
2026-01-13 06:36:31.410 | #1 transferring dockerfile: 539B 0.0s done
2026-01-13 06:36:31.410 | #1 DONE 0.0s
2026-01-13 06:36:31.416 | Containerfile:10
2026-01-13 06:36:31.416 | --------------------
2026-01-13 06:36:31.416 |    8 |     USER root
2026-01-13 06:36:31.416 |    9 |     ENV R_LIBS_USER="/usr/local/lib/R/site-library"
2026-01-13 06:36:31.416 |   10 | >>> apt-get update
2026-01-13 06:36:31.416 |   11 |     apt-get install -y libcurl4-openssl-dev
2026-01-13 06:36:31.416 |   12 |     
2026-01-13 06:36:31.416 | --------------------
2026-01-13 06:36:31.416 | error: failed to solve: dockerfile parse error on line 10: unknown instruction: apt-get

Reproducer

curl --location 'https://wave.seqera.io/v1alpha2/container' \
--header 'Content-Type: application/json' \
--data '{
"packages": {
"type": "CRAN",
"entries": [
"dplyr",
"ggplot2",
"bioc::GenomicRanges"
],
"channels": [
"cran",
"bioconductor"
],
"cranOpts": {
"rImage": "rocker/r-ver:4.4.1",
"basePackages": "littler r-cran-docopt",
"commands": [
"apt-get update",
"apt-get install -y libcurl4-openssl-dev"
]
}
},
"format": "d",
"containerPlatform": "linux/amd64"
}'

detailed build:
https://wave.seqera.io/view/builds/bd-52cc233dfe45b950_1

[ewels]

The Dockerfile looks wrong:

FROM rocker/r-ver:4.4.1
RUN \
    R -e "options(repos = c(CRAN = 'https://cloud.r-project.org/')); options(BioC_mirror = 'https://bioconductor.org/')" \
    && apt-get update && apt-get install -y littler r-cran-docopt \
    && install2.r 'dplyr' 'ggplot2' BiocManager::install('GenomicRanges') \
    && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
    && rm -rf /var/lib/apt/lists/*
USER root
ENV R_LIBS_USER="/usr/local/lib/R/site-library"
apt-get update
apt-get install -y libcurl4-openssl-dev

Specifically, the last two lines, which aren't prefixed by RUN:

apt-get update
apt-get install -y libcurl4-openssl-dev

Also we already ran apt-get update further up so no need to run it a second time.

[pditommaso]

The commands is meant to carry out any Dockerfile command, so RUN needs to be specified in the command

[pditommaso]

Added tests #960

[munishchouhan]

ok i think we need to specify the same in docs too

[munishchouhan]

updated docs for this
#961

[ewels]

Can we also add a validation step in Wave that checks that we have valid prefixes? It'd be nice to get an immediate informative error instead of a build failure.

[munishchouhan]

Can we also add a validation step in Wave that checks that we have valid prefixes? It'd be nice to get an immediate informative error instead of a build failure.

done PR created for doc chnages and command validation
#961