Rserve Docker Image

Docker image for Rserve with Bioconductor packages (DESeq2, SummarizedExperiment), SpiecEasi, VEuPathDB utilities (plot.data, veupathUtils, microbiomeComputations), and other R packages commonly used for microbiome and genomic data analysis.

Based on rocker/r-ver:4.4.2 (R 4.4.2 on Ubuntu 24.04).

Prerequisites

• Docker installed and running
• (Optional) GitHub Personal Access Token for extended debugging needing repeated build cycles and frequent GitHub pulls

Building the Image

Standard Build

If you're in the this directory:

docker build -t rserve .

Using --no-cache

R package installations can fail silently or cache incomplete builds. Using --no-cache ensures a clean build during debugging (but takes longer, of course):

docker build -t rserve . --no-cache

Development Build (with GitHub PAT)

For frequent development builds, provide a GitHub Personal Access Token to avoid API rate limits (60 unauthenticated vs 5000 authenticated requests/hour):

docker build --build-arg GITHUB_PAT=$GITHUB_TOKEN -t rserve .

Note: The PAT is passed as a build argument (ARG) and is not stored in the final image layers. It's only used during the build process.

When to use:

• Development/debugging with frequent rebuilds
• When you hit GitHub API rate limit errors during build (typically opaque error messages at package download time)

When to skip:

• CI/Jenkins builds (usually work fine without it, assuming no rate limit issues)
• Production builds (if rate limits aren't a concern)

Reading/keeping the build log

The pretty progress output is not useful for spotting R installation errors. Use a flat version sent to a file:

docker build --build-arg GITHUB_PAT=$GITHUB_TOKEN --no-cache -t rserve . 2>&1 | tee /tmp/docker-build-attempt-01.log

You can watch it scroll and/or inspect the tmp file with less/grep etc. in another terminal.

Running the Container

Run Rserve Service

Start Rserve daemon listening on port 6311:

docker run --rm rserve:latest

Or with port mapping:

docker run --rm -p 6311:6311 rserve:latest

Interactive R Shell

Get an interactive R shell for testing packages:

docker run --rm -it rserve R

Example session:

> library(DESeq2)
> library(SpiecEasi)
> packageVersion("veupathUtils")

Bash Shell

Get a bash shell for debugging:

docker run --rm -it rserve /bin/bash

Installed Packages

Core Packages

• Rserve (1.8-9): R server for remote R sessions
• plot.data (v5.6.5): VEuPathDB plotting utilities
• microbiomeComputations (v5.1.6.5): Microbiome analysis functions, includes Maaslin2
• veupathUtils (v2.9.0): VEuPathDB utility functions

Bioconductor Packages

• DESeq2: Differential gene expression analysis
• SummarizedExperiment: Container for genomic data
• S4Vectors, IRanges, GenomeInfoDb: Core Bioconductor infrastructure

Network Analysis

• SpiecEasi (v1.0.7): Sparse Inverse Covariance for Ecological Statistical Inference

CRAN Packages

• Data manipulation: dplyr, data.table, readr
• Utilities: jsonlite, bit64, digest, Hmisc, Rcpp, remotes

Troubleshooting

S4Vectors/DESeq2 Compilation Errors

Problem

When building on Ubuntu 24.04 with gcc 13.3.0 and R 4.4.2 (rocker/r-ver:4.4.2), S4Vectors compilation fails with:

error: format not a string literal and no format arguments [-Werror=format-security]

This cascading failure prevents installation of packages that depend on S4Vectors:

• "Skipping 1 packages not available: Seqinfo"
• "packages 'Seqinfo' are not available"
• "ERROR: dependency 'IRanges' is not available for package 'GenomeInfoDb'"
• "ERROR: dependency 'SummarizedExperiment' is not available for package 'DESeq2'"

Root Cause

Bioconductor S4Vectors code calls error(variable) instead of the correct error("%s", variable) format. Ubuntu 24.04's default compiler flags include -Werror=format-security, which treats this as a fatal error rather than a warning.

Dependency chain: S4Vectors → IRanges → GenomeInfoDb → SummarizedExperiment → DESeq2

This is a long-standing issue in the Bioconductor codebase (since 2013+) that affects various Ubuntu versions with strict compiler security settings.

Solution

Override CFLAGS in ~/.R/Makevars to remove -Werror=format-security while keeping other security flags:

In Dockerfile (see lines 19-27):

RUN mkdir -p /root/.R && \
    echo "CFLAGS = -g -O2 -fstack-protector-strong -Wformat -Wdate-time -D_FORTIFY_SOURCE=2" > /root/.R/Makevars

For local R installation:

mkdir -p ~/.R
echo "CFLAGS = -g -O2 -fstack-protector-strong -Wformat -Wdate-time -D_FORTIFY_SOURCE=2" > ~/.R/Makevars

This removes -Werror=format-security from the default rocker/r-ver:4.4.2 flags while preserving other security features:

• Default flags: -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
• Our override: -g -O2 -fstack-protector-strong -Wformat -Wdate-time -D_FORTIFY_SOURCE=2 (removed -Werror=format-security)

Affected Environments

• Ubuntu 24.04
• gcc 13.3.0
• R 4.4.2
• rocker/r-ver:4.4.2
• Bioconductor packages: S4Vectors, IRanges, GenomeInfoDb, SummarizedExperiment, DESeq2

Search Keywords

If you encountered this issue, you may have searched for:

• "S4Vectors compilation error"
• "S4Vectors compilation failed"
• "DESeq2 won't install"
• "DESeq2 installation error Ubuntu"
• "Bioconductor package won't compile"
• "IRanges compilation error"
• "GenomeInfoDb installation fails"
• "SummarizedExperiment installation fails"
• "error: format not a string literal and no format arguments"
• "Werror=format-security"
• "Bioconductor format-security"
• "Seqinfo not available"
• "packages 'Seqinfo' are not available"
• "Skipping 1 packages not available: Seqinfo"

GitHub Rate Limits

If you encounter GitHub API rate limit errors during build:

Error: Failed to install 'unknown package' from GitHub:
  HTTP error 403.
  API rate limit exceeded

Solution: Use a GitHub Personal Access Token (see "Development Build" section above).

Notes

• This image uses specific package versions for reproducibility:
  • plot.data: v5.6.5
  • microbiomeComputations: v5.1.6.5 (includes Maaslin2 and veupathUtils v2.9.0)
  • SpiecEasi: v1.0.7
• The S4Vectors compilation workaround should be removed once Bioconductor fixes their code
• Rserve listens on port 6311 by default
• Configuration file: /etc/Rserv.conf
• Working directory: /opt/rserve/work
• Library files: /opt/rserve/lib