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dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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Running dyno fails #104

Open jingshuw opened 3 years ago

jingshuw commented 3 years ago

Hello,

We have run dyno earlier and it was successful. However, recently, the infer_trajectory function keeps giving errors. We tried to reinstall everything and install dyno on new computers, but still can not get it to run successfully. Here is the error message:

library(dyno) library(tidyverse) 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_paga_tree:v0.9.9.06' echo hi Error in rethrow_call(c_processx_exec, command, c(command, args), stdin, : cannot start processx process (system error 2, No such file or directory) @unix/processx.c:573

Other messages that we have encountered after running the infer_trajectory() functions are

error in processx::run(“docker”, c(“images”, paste0(“--format=“, format), : System command ‘docker’ failed, exit status: 1, stderr: E> Error response from daemon: dial unix docker.raw.sock: connect: connection refused Type .Last.error.trace to see where the error occured In addition: Warning message: In dir.create(file.path(save_path, filename)) : ‘./labels/dentate’ already exists

and

Error in stringr::strreplace(., “^ti“, “”) : lazy-load database ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/stringi/R/stringi.rdb’ is corrupt In addition: Warning message: In stringr::strreplace(., “^ti“, “”) : internal error -3 in R_decompress1

It would be really helpful if you can address these issues.

Best, Jingshu

Woqo commented 3 years ago

I think you should use firstly: docker pull to get docker container