R packages cannot find tzdata because TZDIR not set

[tjbencomo]

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

R packages like readr that rely on tzdata fail to find tzdata when running in a Snakemake workflow using a Mambaforge singularity container and conda environment.

StackOverflow Issue

This problem is remedied by setting TZDIR at the beginning of R scripts before loading packages:

Sys.setenv("TZDIR"=paste0(Sys.getenv("CONDA_PREFIX"), "/share/zoneinfo"))
library(readr)

It has been suggested tzdata set TZDIR to point to $CONDA_PREFIX/share/zoneinfo to remedy this issue

Environment (conda list):

$ conda list

#env.yml
name: env
channels:
    - default
    - bioconda
    - conda-forge
dependencies:
    - r-readr
    - tzdata

Details about conda and system ( conda info ):

$ conda info

[drhagen]

I have this issue too. I almost made an issue on r-lubridate before realizing that this is probably the correct place to fix this. If tzdata is installed in the conda environment, then I definitely want everything in the environment that understands the TZDIR variable to use this package.

[h-vetinari]

For R in particular, there's also a package called r-tzdb which might be easier to interface with. It ships more than just tzdata (AFAIU also tzcode), but also some R-specific things.