infer_trajectory returns nothing

[alexQiSong]

Hi,

I've tried to use infer_trajecotry() for the example dataset but got nothing returned from the function. Below is what I did:

> 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 1.3.1 ──
✓ ggplot2 3.3.3     ✓ purrr   0.3.4
✓ tibble  3.1.1     ✓ dplyr   1.0.6
✓ tidyr   1.1.3     ✓ stringr 1.4.0
✓ readr   1.4.0     ✓ forcats 0.5.1
── Conflicts ──────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
> data("fibroblast_reprogramming_treutlein")
> 
> dataset <- wrap_expression(
+   counts = fibroblast_reprogramming_treutlein$counts,
+   expression = fibroblast_reprogramming_treutlein$expression
+ )
> model <- infer_trajectory(dataset, "slingshot")

> model
Error: object 'model' not found

I've checked the installation of singularity. Everything looks good...

> dynwrap::test_singularity_installation(detailed = TRUE)
✔ Singularity is installed
✔ Singularity is at correct version (>=3.0): 3.5.2 is installed
✔ Singularity can pull and run a container from Dockerhub
✔ Singularity can mount temporary volumes
✔ Singularity test successful ------------------------------------------------------------
[1] TRUE

Would appreciate any help. Thanks a lot.

Qi

[alexQiSong]

I used verbose = True for infer_trajectory() then it produced the error message saying hdf5r is not installed. So I installed the package and this issue is resolved.

Perhaps this is because the installation step does not require 'hdf5r' but it is actually required for running inference?