Using R in a Snakemake workflow with Mambaforge - r

Question

I'm building a pipeline with Snakemake. One rule involves an R script that reads a CSV file using readr. I get this error when I run the pipeline with --use-singularity and --use-conda
Error: Unknown TZ UTC
In addition: Warning message:
In OlsonNames() : no Olson database found
Execution halted
Google suggests readr is crashing due to missing tzdata but I can't figure out how to install the tzdata package and make readr see it. I am running the entire pipeline in a Mambaforge container to ensure reproducibility. Snakemake recommends using Mambaforge over a Miniconda container as it's faster, but I think my error involves Mambaforge as using Miniconda solves the error.
Here's a workflow to reproduce the error:
#Snakefile
singularity: "docker://condaforge/mambaforge"
rule targets:
input:
"out.txt"
rule readr:
input:
"input.csv"
output:
"out.txt"
conda:
"env.yml"
script:
"test.R"
#env.yml
name: env
channels:
- default
- bioconda
- conda-forge
dependencies:
- r-readr
- tzdata
#test.R
library(readr)
fp <- snakemake#input[[1]]
df <- read_csv(fp)
print(df)
write(df$x, "out.txt")
I run the workflow with snakemake --use-conda --use-singularity. How do I run R scripts when the Snakemake workflow is running from a Mambaforge singularity container?

Answer 1

Looking through the stack of R code leading to the error, I see that it checks a bunch of default locations for the zoneinfo folder that tzdata includes, but also checks for a TZDIR environment variable.
I believe a proper solution to this would be for the Conda tzdata package to set this variable to point to it. This will require a PR to the Conda Forge package (see repo issue). In the meantime, one could do either of the following as workarounds.
Workaround 1: Set TZDIR from R
Continuing to use the tzdata package from Conda, one could set the environment variable at the start of the R script.
#!/usr/bin/env Rscript
## the following assumes active Conda environment with `tzdata` installed
Sys.setenv("TZDIR"=paste0(Sys.getenv("CONDA_PREFIX"), "/share/zoneinfo"))
I would consider this a temporary workaround.
Workaround 2: Derive a New Docker
Otherwise, make a new Docker image that includes a system-level tzdata installation. This appears to be a common issue, so following other examples (and keeping things clean), it'd go something like:
Dockerfile
FROM --platform=linux/amd64 condaforge/mambaforge:latest
## include tzdata
RUN apt-get update > /dev/null \
&& DEBIAN_FRONTEND="noninteractive" apt-get install --no-install-recommends -y tzdata > /dev/null \
&& apt-get clean
Upload this to Docker Hub and use it instead of the Mambaforge image as the image for Snakemake. This is probably a more reliable long-term solution, but perhaps not everyone wants to create a Docker Hub account.