FATAL error using dyno on HPC with singularity

[FERWoods]

Hi there - I'm trying to run dyno on a HPC and running into an issue with pulling docker images -- see below full log from R terminal. This is run from within a conda environment (also below) due to requiring a later R version (4.2) than available on cluster. Grateful for any advice/debugging options -- the error seems to relate to a connection problem with the docker registry. I thought perhaps this was due to a firewall issue on the HPC but I cannot ping the registry or IP listed on my local pc either.

Grateful for any advice.
Thanks,
Freya

R environ:

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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Platform: x86_64-conda-linux-gnu (64-bit)

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library(dyno)
Loading required package: dynfeature
Loading required package: dynguidelines
Loading required package: dynmethods
Loading required package: dynplot
Loading required package: dynwrap

library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0 ✔ purrr 1.0.1
✔ tibble 3.1.8 ✔ dplyr 1.0.10
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 1.0.0
── Conflicts ────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
Warning messages:
1: package ‘tidyverse’ was built under R version 4.2.1
2: package ‘ggplot2’ was built under R version 4.2.2
3: package ‘tibble’ was built under R version 4.2.1
4: package ‘tidyr’ was built under R version 4.2.2
5: package ‘readr’ was built under R version 4.2.1
6: package ‘purrr’ was built under R version 4.2.2
7: package ‘dplyr’ was built under R version 4.2.1
8: package ‘stringr’ was built under R version 4.2.2
9: package ‘forcats’ was built under R version 4.2.2
data("fibroblast_reprogramming_treutlein")

dataset <- wrap_expression(
counts = fibroblast_reprogramming_treutlein$counts,
expression = fibroblast_reprogramming_treutlein$expression
)

model <- infer_trajectory(dataset, "slingshot")
Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi
Running /usr/bin/singularity exec --containall -B
'/scratch/kvfg350/Rtmpp9XpHZ/file69b94eb6914b/:/copy_mount,/scratch/kvfg350/Rtmpp9XpHZ/file69b926890f26/tmp:/tmp2'
'docker://dynverse/ti_slingshot:v1.0.3' cp /code/definition.yml
/copy_mount/
FATAL: Unable to handle docker://dynverse/ti_slingshot:v1.0.3 uri: failed to get checksum for docker://dynverse/ti_slingshot:v1.0.3: error pinging docker registry registry-1.docker.io: Get "https://registry-1.docker.io/v2/": dial tcp 18.215.138.58:443: i/o timeout
Error in map():
ℹ In index: 1.
! FATAL: Unable to handle docker://dynverse/ti_slingshot:v1.0.3 uri: failed to get checksum for docker://dynverse/ti_slingshot:v1.0.3: error pinging docker registry registry-1.docker.io: Get "https://registry-1.docker.io/v2/": dial tcp 18.215.138.58:443: i/o timeout

conda.yaml file, in case of interest:
channels:

• conda-forge
• bioconda
  dependencies:
• r-base=4.2.0
• r-devtools=2.4.5
• r-usethis=2.1.6
• r-Seurat=4.3.0
• r-tidyverse=1.3.2
• r-BiocManager=1.30.19
• r-dplyr=1.0.10
• bioconductor-FlowSOM
• bioconductor-flowCore
• bioconductor-flowWorkspace
• bioconductor-flowViz
• bioconductor-flowStats
• bioconductor-monocle