nei() was deprecated in igraph 2.1.0 and is now defunct.

[kuangquanxing]

What happens, and what did you expect instead?

nei() was deprecated in igraph 2.1.0 and is now defunct.
ℹ Please use .nei() instead.

To reproduce

nei() was deprecated in igraph 2.1.0 and is now defunct.

System information

No response

[maelle]

@kuangquanxing yes this is expected. How did you get the error? If you provide us with a reproducible example, we can help you fix it (it should only be a matter of replacing nei() with .nei(), unless the function is used in a package you don't own).

[dane113]

cds <- orderCells(cds)
Error:
! nei() was deprecated in igraph 2.1.0 and is now defunct.
ℹ Please use .nei() instead.

[szhorvat]

orderCells is not an igraph function. You are probably using a different package that has not been updated to work with recent versions of igraph. Please contact the maintainers of the other package.

If this function is not from another package but your own code, you need to do precisely what the error message tells you: replace nei() with .nei() in your code.

[dane113]

When performing trajectory analysis with Monocle, if you encounter the error "orderCells is not an igraph function", it is likely due to an incompatibility between Monocle and the installed version of igraph. How can I resolve this issue? Thank you.

…

2025年2月8日 19:41，Szabolcs Horvát ***@***.***> 写道： orderCells is not an igraph function. You are probably using a different package that has not been updated to work with recent versions of igraph. Please contact the maintainers of the other package. If this function is not from another package but your own code, you need to do precisely what the error message tells you: replace nei() with .nei() in your code. —

[szhorvat]

This should be fixed in Monocle. I suggest you contact the Monocle developers about it. If Monocle is no longer maintained, then you can install an older version of igraph (a version older than 2.1.0). However, this is not ideal, as you will miss out on some bugfixes.