Hi,
I'm using a container built on seqera with:
channels:
- conda-forge
- bioconda
dependencies:
- conda-forge::r-data.table=1.17.8
- conda-forge::r-janitor=2.2.1
- conda-forge::r-r.utils=2.13.0
- conda-forge::r-nfcore.utils=0.0.2
This library janitor calls lubridate that needs /etc/localtime.
I then obtain the warning:
INFO: Converting SIF file to temporary sandbox...
WARNING: underlay of /etc/localtime required more than 50 (74) bind mounts
Warning: Your system is mis-configured: '/etc/localtime' is not a symlink
Warning: '/etc/localtime' is not identical to any known timezone fileThis warning appears in other containers (5 match on Nextflow slack and 10 on nf-core), it is then converted to an error in my nf-core module when I do library(janitor).
I've fixed it by adding Sys.setenv(TZ = "UTC") in my R script but I was wondering if a solution could be found at the container building level.
Hi,
I'm using a container built on seqera with:
This library
janitorcallslubridatethat needs /etc/localtime.I then obtain the warning:
INFO: Converting SIF file to temporary sandbox... WARNING: underlay of /etc/localtime required more than 50 (74) bind mounts Warning: Your system is mis-configured: '/etc/localtime' is not a symlink Warning: '/etc/localtime' is not identical to any known timezone fileThis warning appears in other containers (5 match on Nextflow slack and 10 on nf-core), it is then converted to an error in my nf-core module when I do
library(janitor).I've fixed it by adding Sys.setenv(TZ = "UTC") in my R script but I was wondering if a solution could be found at the container building level.