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"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
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")
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" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
library(dyno) Loading required package: dynfeature Loading required package: dynguidelines Loading required package: dynmethods Loading required package: dynplot Loading required package: dynwrap
dataset <- wrap_expression( counts = fibroblast_reprogramming_treutlein$counts, expression = fibroblast_reprogramming_treutlein$expression )
conda.yaml file, in case of interest: channels: