orderCells function fails due to deprecated nei() call**

[weissnichtwo]

Description:
When I run the orderCells function, I encounter an error because it is trying to call the nei() function, which has been deprecated in igraph version 2.1.0 and is now defunct.

Steps to reproduce:

1. Load the monocle and igraph libraries.
2. Create a CDS object (e.g., mycds).
3. Run mycds <- orderCells(mycds).

Error message:
! nei() was deprecated in igraph 2.1.0 and is now defunct.
ℹ Please use .nei() instead.
Run rlang::last_trace() to see where the error occurred.

Expected behavior:
The orderCells function should run without errors and return the ordered cells.

Actual behavior:
The function fails with the above-mentioned error message.

Session info:

• R version: 4.4.1
• monocle version: 2.32.0
• igraph version: 2.1.1

Reproducible example:

library(igraph)
library(monocle)

# Assuming mycds is a valid CDS object
mycds <- orderCells(mycds)
Thank you for your help!

[szhaoaf]

As the error said, ! nei() was deprecated in igraph 2.1.0 and is now defunct. The igraph version: 2.1.1 version accounts for the error.

To solve this issue, simply downgrading igraph can work.

https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/igraph_2.0.3.tgz

Go to above link and install the 2.0.3 version, restart the R session. Then it solved for me.

> gbm_cds <- orderCells(gbm_cds)
Warning messages:
1: In dfs(graph = graph, root = root, mode = mode, unreachable = unreachable,  :
  Argument `neimode' is deprecated; use `mode' instead
2: In dfs(graph = graph, root = root, mode = mode, unreachable = unreachable,  :
  Argument `neimode' is deprecated; use `mode' instead

Session info:

sessionInfo()
R version 4.4.1 (2024-06-14)
monocle_2.32.0
igraph_2.0.3

Bests

[maelle]

In which package is nei() used? In that package, it can simply be replaced by .nei() which is the name of the function in igraph. Happy to make a PR to the relevant repository if you give me the link. 😸

[Hunkhuyu]

cds<- orderCells(cds, root_state = NULL, num_paths = NULL, reverse = NULL)
error in lazy_dots(..., .follow_symbols = FALSE):
comand not found 'make_lazy_dots'
(the problem then i meet)

[maelle]

@Hunkhuyu I'm sorry to hear about that. Would you mind preparing a small reproducible example so I might look into it more efficiently? See https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html Thank you!

[szhorvat]

@Hunkhuyu There is no make_lazy_dots in igraph 2.1.1. If you see such an error, you must be using an older version. Make sure you are using the latest version.

[szhaoaf]

In which package is nei() used? In that package, it can simply be replaced by .nei() which is the name of the function in igraph. Happy to make a PR to the relevant repository if you give me the link. 😸

Dear Maelle,

Thank you for your information and sorry to miss your reply.
I guess it would be one of the below packages using .nei() function.

detach("package:igraph", unload = TRUE)
Warning message:
‘igraph’ namespace cannot be unloaded:
namespace ‘igraph’ is imported by ‘leiden’, ‘leidenbase’, ‘monocle’, ‘Seurat’ so cannot be unloaded

To be more precise, when running Monocle2 with the lastest version igraph (or igraph version > 2.1.0; mine is 2.1.1), the error will appear as below:

gbm_cds <- orderCells(gbm_cds)
Error:
! nei() was deprecated in igraph 2.1.0 and is now defunct.
ℹ Please use .nei() instead.
Run rlang::last_trace() to see where the error occurred.

As suggested by the error, I just downgraded my igraph into igraph 2.0.3 as I mentioned in previous comments. Restart R, it solved the error.

gbm_cds <- orderCells(gbm_cds)
Warning messages:
1: In dfs(graph = graph, root = root, mode = mode, unreachable = unreachable, :
Argument neimode' is deprecated; use mode' instead
2: In dfs(graph = graph, root = root, mode = mode, unreachable = unreachable, :
Argument neimode' is deprecated; use mode' instead

Best,
szhaoaf

[orange511]

As the error said, ! nei() was deprecated in igraph 2.1.0 and is now defunct. The igraph version: 2.1.1 version accounts for the error.

To solve this issue, simply downgrading igraph can work.

https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/igraph_2.0.3.tgz

Go to above link and install the 2.0.3 version, restart the R session. Then it solved for me.

> gbm_cds <- orderCells(gbm_cds)
Warning messages:
1: In dfs(graph = graph, root = root, mode = mode, unreachable = unreachable,  :
  Argument `neimode' is deprecated; use `mode' instead
2: In dfs(graph = graph, root = root, mode = mode, unreachable = unreachable,  :
  Argument `neimode' is deprecated; use `mode' instead

Session info:

sessionInfo()
R version 4.4.1 (2024-06-14)
monocle_2.32.0
igraph_2.0.3

Bests

It works!
Thank you very much!